Mercurial > repos > stef > falco
changeset 39:a793ffd0cd04 draft
Uploaded
| author | stef |
|---|---|
| date | Tue, 23 Dec 2014 11:26:33 -0500 |
| parents | f1b32c09deaf |
| children | e9ba05d7b228 |
| files | README.rst falco-call.sh falco-call.xml falco-report.sh falco-report.xml falco/README falco/amplicon-Al-TSACP.sh falco/amplicon-AlVcAn-HaloPlex.sh falco/amplicon-AlVcAn-TSACP.sh falco/amplicon-QC.sh falco/amplicon-Report.sh falco/amplicon-VcAn-TSACP.sh falco/bin/falco falco/bin/fastq_quality_trimmer falco/data/HCT-116/HCT116.bam falco/data/HCT-116/HCT116.bam.bai falco/init.sh falco/lib/R/addQual.R falco/lib/R/func.R falco/lib/perl/perAmpliconAnalysis.pl falco/lib/perl/qc2vcf.pl falco/lib/perl/qcFilt.pl falco/misc/addQc.pl falco/misc/addQual.R falco/misc/alignmentStats.pl falco/misc/attachGff.pl falco/misc/attachManifest.pl falco/misc/checkRunComplete.pl falco/misc/errorRate.pl falco/misc/filter.R falco/misc/filter.pl falco/misc/filterQC.R falco/misc/func.R falco/misc/getData.pl falco/misc/mkHtmlReport.pl falco/misc/pairUp.pl falco/misc/perAmpliconAnalysis.pl falco/misc/pileup2cov.pl falco/misc/plots.R falco/misc/plotsPng.R falco/misc/plotsQC.R falco/misc/qc2vcf.pl falco/misc/qcFilt.pl falco/misc/report.sh falco/misc/splitEff.pl falco/misc/startAnalysis.pl falco/misc/varFilter.pl falco/misc/vcf2tsv.pl falco/ref/TSACP/TSACP.bed falco/ref/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt falco/ref/TSACP/TruSeq_Custom_Amplicon_Control_Manifest_ACP1.txt falco/ref/TSACP/tobed.pl falco/ref/TSACP/truseq_amplicon_cancer_panel_manifest_afp1_pn15032433_b.txt falco/ref/filters/README falco/ref/filters/filter.tsv tool-data/GALAXY_EGFR.bed~ tool-data/GALAXY_TSACP.bed tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt tool_dependencies.xml |
| diffstat | 58 files changed, 9107 insertions(+), 5242 deletions(-) [+] |
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--- a/README.rst Fri Oct 10 11:28:57 2014 -0400 +++ b/README.rst Tue Dec 23 11:26:33 2014 -0500 @@ -1,21 +1,35 @@ -Falco Amplicon Analysis Pipeline & Galaxy wrapper +FALCO Amplicon Analysis Pipeline & Galaxy wrapper ======================================== -Text +FALCO variant-caller is part of the Amplicon Analysis Pipeline (AAP). + +The typical workflow is as follows: +* paired-end amplicon sequencing +* merge pairs by overlapping them +* map the single read fastq with BWA +* perform variant calling with FALCO +* create (html) report of the results + +FALCO uses samtools and straight-forward statistics to determine wether a +potential variant is likely a (technical) artifact or not. + +Input / Output +======= + +Input of the caller is a BAM file, output VCF History ======= -============== ======================================================================== +============== ================================================================ Date Changes --------------- ------------------------------------------------------------------------ -September 2014 * first release in Tool Shed -July 2014 * first release in Test Tool Shed -============== ======================================================================== +-------------- ---------------------------------------------------------------- +December 2014 * first release in Test Tool Shed +============== ================================================================ Bug Reports & other questions ============================= -Issues can be reported via the contact form at +Issues can be reported via http://www.tgac.nl/
--- a/falco-call.sh Fri Oct 10 11:28:57 2014 -0400 +++ b/falco-call.sh Tue Dec 23 11:26:33 2014 -0500 @@ -1,7 +1,7 @@ #!/bin/bash TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -echo "Start falco sh" +echo "Started FALCO calling" ## ---------- ## Variables setup @@ -13,105 +13,51 @@ ## ---------- ## Create extra init script ## ---------- -if [ $design_file != 'None' ] # Galaxy default is "None" +if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default somehow is "None" then - BED_PATH=$design_file + FILTER_PARAM=" --filter "$filter_file else - BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" -fi - -if [ $manifest_file != 'None' ] # Galaxy default is "None" -then - MAN_PATH=$manifest_file -else - MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" + FILTER_PARAM="" fi -echo "BED:"$design_file -echo "MAN:"$manifest_file -echo "BED chosen:"$BED_PATH -echo "MAN chosen:"$MAN_PATH -#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH -#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH - -init_file="galaxy_init.sh" -echo '#!/bin/bash' > $init_file - -## executables -#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file -#echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file -#echo "snpSift=/ccagc/lib/SnpSift" >> $init_file -#echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file -#echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file -#echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file -echo "samtools=samtools" >> $init_file -echo "bcftools=bcftools" >> $init_file - -## files -echo "targetBed=$BED_PATH" >> $init_file -echo "manifest=$MAN_PATH" >> $init_file +if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" +then + MANIFEST_PARAM=" --manifest "$manifest_file +else + MANIFEST_PARAM="" +fi ## ---------- ## Status / debug ## ---------- -echo "BAM: "$bam_file -echo "OUT: "$bam_name -echo "BAMBASE: "$bam_base -#echo "OUTPATH: "$out_path -#echo "HTMLOUT: "$html_out -echo "VCFOUT : "$vcf_out -echo "INIT : "$init_file - -echo "------ sourcing init_file" -source $init_file - -#echo "------ --- ------" -#echo "------ sam ------" -#echo "------ --- ------" -#$samtools -#echo "------ --- ------" -#echo "------ bcf ------" -#echo "------ --- ------" -#$bcftools -#echo "--- snpsift ---" -#java -jar $snpSift/SnpSift.jar -#echo "--- snpeff ---" -#java -jar $snpEff/snpeff.jar -#echo "--- varscan ---" -#java -jar $varScan - - - +DEBUG=1 +if [ $DEBUG ] +then + DBS="[INFO] " + echo $DBS"FILTER: "$filter_file + echo $DBS"MANIFES: "$manifest_file + echo $DBS"REFFILE: "$REF_FILE + echo $DBS"DB_KEY: "$DB_KEY + echo $DBS"REF_SRC: "$REF_SOURCE + echo $DBS"BAMFILE: "$bam_file + echo $DBS"BAMNAME: "$bam_name + echo $DBS"BAMBASE: "$bam_base + echo $DBS"OUTPATH: "$out_path +fi ## ---------- ## create output files dir ## ---------- mkdir $out_path -mkdir $out_path/$bam_base ## ---------- ## running analysis ## ---------- - -## DEBUG -#exit 0 -echo "Starting VcAn" -$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base -echo "...done with VcAn" -#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more - -#echo "Starting amplicon-Report" -#$TOOLDIR/falco/amplicon-Report.sh $bam_base - -#echo "Starting QC" -#$TOOLDIR/falco/amplicon-QC.sh $bam_file - -#echo "Starting plots.R" -#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf - -#echo "Starting mkHtmlReport" -#$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./ - +echo "Starting variant calling" +CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM" +echo "[INFO] "$CALL_STRING +perl $CALL_STRING +echo "...done with variant calling" ## ---------- @@ -128,14 +74,15 @@ echo "</head>" >> $html_out echo "<body>" >> $html_out echo " <h1>FALCO</h1>" >> $html_out -echo " <a href=\"index.html\">HTML</a>" >> $html_out +echo " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p>" >> $html_out +#echo " <a href=\"index.html\">HTML</a>" >> $html_out echo " <table><tbody>" >> $html_out -#for file in *.vcf *.txt *.tsv -for file in * +for file in *.vcf *.txt *stderr *stdout +#for file in * do lineCount=`wc -l $file | cut -f 1 -d " "` echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out - #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out + echo " <tr><td> --> " `head -1 $file` "</td></tr>" >> $html_out done echo " </tbody></table>" >> $html_out echo "</body>" >> $html_out @@ -146,14 +93,14 @@ ## ---------- #cp 'index.html' $html_out # this is the overview of samples html #cp $bam_base'.html' $out_path/'out.html' # this is the sample html -cp $bam_base'.vcf' $vcf_out +cp $bam_base'.falco.vcf' $vcf_out ## ---------- ## copy files to keep to output path ## ---------- #cp -r ./$bam_base/*png $out_path/$bam_base/ #cp -r ./* $out_path -#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path +cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path ## ---------- echo "END falco sh"
--- a/falco-call.xml Fri Oct 10 11:28:57 2014 -0400 +++ b/falco-call.xml Tue Dec 23 11:26:33 2014 -0500 @@ -6,48 +6,16 @@ <requirement type="package" version="3.1.0">R</requirement> <requirement type="package" version="2">bcftools</requirement> <!-- - <requirement type="package" version="3.4">snpeff</requirement> - <requirement type="package" version="2">varscan</requirement> - + <requirement type="set_environment">TOOL_DIR</requirement> --> - <!-- - - <requirement type="set_environment">JAVA_JAR_PATH</requirement> - <requirement type="set_environment">SNPEFF_JAR_PATH</requirement> - - <requirement type="set_environment">JAR_PATH1</requirement> - <requirement type="set_environment">JAR_PATH2</requirement> - --> - <requirement type="set_environment">TOOL_DIR</requirement> </requirements> <description>FALCO: Amplicon Analysis Pipeline</description> - - <!-- command block to call script with specific R installation (set full paths) --> - <!-- - <command> - /full/path/to/Rscript - /full/path/to/QDNAseq.R - $qdnaseq_cfg - </command> - --> - <!-- command block to call script with default R environment --> <command interpreter="bash"> - <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &&; echo "ECHO PRINT"; --> - <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; --> falco-call.sh $falco_cfg; </command> - <!-- - <command interpreter="bash"> - falco/amplicon-VcAn-TSACP.sh $bam $bam.name; - echo "DONE" - </command> - <command interpreter="perl"> - falco.pl $htmlFile ${htmlFile.files_path} $bam $bam.name; - </command> - --> <stdio> <!-- Anything higher than 0 means the bash script didnt finish --> @@ -58,14 +26,31 @@ <!-- ==================== --> <!-- General inputs --> <!-- ==================== --> + <conditional name="genomeSource"> + <param name="refGenomeSource" type="select" label="You can select a reference genome from your history or use a built-in index"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from history</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select a reference genome"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available in table" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> + </when> + </conditional> + <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST"> <validator type="empty_field" /> <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator> </param> <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" /> - <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/> - <param format="bed" name="design_file" optional="True" type="data" label="BED File" help="When left empty, default Cancer Panel is used"/> + <param format="tsv" name="filter_file" optional="True" type="data" label="FILTER File" help="When left empty, default list of genomic positions is used"/> <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/> <!-- ==================== --> @@ -79,27 +64,32 @@ <!-- ==================== --> <configfiles> <configfile name="falco_cfg"> - design_file=$design_file + filter_file=$filter_file manifest_file=$manifest_file bam_file=$bam bam_name=$bam.name html_out=$html_output vcf_out=$vcf_output - out_path=${vcf_output.files_path} + out_path=${html_output.files_path} + ## reference source + REF_SOURCE="${genomeSource.refGenomeSource}" + #if $genomeSource.refGenomeSource == "history": + ##build index on the fly + REF_FILE="${genomeSource.ownFile}" + DB_KEY="${dbkey}" + #else: + ##use precomputed indexes + REF_FILE="${genomeSource.indices.fields.path}" + #end if </configfile> </configfiles> - <!-- - jar_path1=$JAR_PATH1 - jar_path2=$JAR_PATH2 - jar_path3=$JAVA_JAR_PATH - jar_path4=$SNPEFF_JAR_PATH - --> + <!-- ==================== --> <!-- Main output is an html based report, additional on request --> <!-- ==================== --> <outputs> - <data format="html" name="html_output" label="FALCO AAP (${jobName})" /> - <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" /> + <data format="html" name="html_output" label="FALCO-calling (${jobName})" /> + <data format="vcf" name="vcf_output" label="FALCO-calling (${jobName}): VCF" /> </outputs> <!-- ==================== --> @@ -120,17 +110,23 @@ **Introduction** -This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_ +This tool is a wrapper for the variant caller FALCO_ which is part of the Amplicon Analysis Pipeline (AAP) -.. _FALCO: https://bitbucket.org/daoud/falco +.. _FALCO: https://github.com/tgac-vumc/falco/ Calls and annotates genomic variants for each amplicon in a design. +**Notes** + +Because each amplicon is considered separate test, if two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon. + ----- **Citation** -For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). +For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). [Pubmed] + +.. _Pubmed: http://www.ncbi.nlm.nih.gov/pubmed/25209392 </help>
--- a/falco-report.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,158 +0,0 @@ -#!/bin/bash -TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -echo "Start falco sh" - -## ---------- -## Variables setup -## ---------- -#bam_file=$1 -#bam_name=$2 -#html_out=$3 -#vcf_out=$4 -#out_path=$5 -source $1 -#JAR_PATH=$3 - -bam_base=`echo $bam_name | sed 's#.bam$##' - ` - -## ---------- -## Create extra init script -## ---------- -#if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi -#if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi -if [ $design_file != 'None' ] # Galaxy default is "None" -then - BED_PATH=$design_file -else - BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" -fi - -if [ $manifest_file != 'None' ] # Galaxy default is "None" -then - MAN_PATH=$manifest_file -else - MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" -fi - -echo "BED:"$design_file -echo "MAN:"$manifest_file -echo "BED chosen:"$BED_PATH -echo "MAN chosen:"$MAN_PATH -#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH -#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH -echo "JAR_PATH1:"$JAR_PATH -#echo "JAR_PATH2:"$jar_path2 - -init_file="galaxy_init.sh" -echo '#!/bin/bash' > $init_file - -## executables -#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file -#echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file -#echo "snpSift=/ccagc/lib/SnpSift" >> $init_file -#echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file -#echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file -#echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file - -## files -echo "targetBed=$BED_PATH" >> $init_file -echo "manifest=$MAN_PATH" >> $init_file - -## ---------- -## Status / debug -## ---------- -echo "BAM: "$bam_file -echo "OUT: "$bam_name -echo "BAMBASE: "$bam_base -echo "OUTPATH: "$out_path -echo "HTMLOUT: "$html_out -echo "VCFOUT : "$vcf_out -echo "INIT : "$init_file - -source $init_file - -echo "--- sam ---" -samtools -echo "--- bcf ---" -bcftools -#echo "--- snpsift ---" -#java -jar $snpSift/SnpSift.jar -#echo "--- snpeff ---" -#java -jar $snpEff/snpeff.jar -#echo "--- varscan ---" -#java -jar $varScan - -exit 0 - -## ---------- -## create output files dir -## ---------- -mkdir $out_path -mkdir $out_path/$bam_base - -## ---------- -## running analysis -## ---------- -echo "Starting VcAn" -$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base -#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more - -echo "Starting amplicon-Report" -$TOOLDIR/falco/amplicon-Report.sh $bam_base - -echo "Starting QC" -$TOOLDIR/falco/amplicon-QC.sh $bam_file - -#echo "Starting plots.R" -#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf - -echo "Starting mkHtmlReport" -$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./ - - - -## ---------- -## create index html for main galaxy output -## ---------- -echo "<!DOCTYPE html>" >> $html_out -echo "<html>" >> $html_out -echo "<head>" >> $html_out -echo "<style>" >> $html_out -echo " body{ padding: 0px 20px; }" >> $html_out -echo " h1{ color: red; }" >> $html_out -echo " table{ border: 1px solid black; padding: 5px }" >> $html_out -echo "</style>" >> $html_out -echo "</head>" >> $html_out -echo "<body>" >> $html_out -echo " <h1>FALCO</h1>" >> $html_out -echo " <a href=\"index.html\">HTML</a>" >> $html_out -echo " <table><tbody>" >> $html_out -#for file in *.vcf *.txt *.tsv -for file in * -do - lineCount=`wc -l $file | cut -f 1 -d " "` - echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out - #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out -done -echo " </tbody></table>" >> $html_out -echo "</body>" >> $html_out -echo "</html>" >> $html_out - -## ---------- -## creating galaxy history outputs -## ---------- -#cp 'index.html' $html_out # this is the overview of samples html -cp $bam_base'.html' $out_path/'out.html' # this is the sample html -cp $bam_base'.vcf' $vcf_out - -## ---------- -## copy files to keep to output path -## ---------- -cp -r ./$bam_base/*png $out_path/$bam_base/ -cp -r ./* $out_path -#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path - -## ---------- -echo "END falco sh" -exit 0 \ No newline at end of file
--- a/falco-report.xml Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,137 +0,0 @@ -<tool id="falco-report" name="falco-report" version="0.0.1"> - - <requirements> - - <requirement type="package" version="0.1.19">samtools</requirement> - - <requirement type="package" version="3.1.0">R</requirement> - <!-- - <requirement type="package" version="3.4">snpeff</requirement> - <requirement type="package" version="2">varscan</requirement> - <requirement type="package" version="2">bcftools</requirement> - --> - <!-- - - <requirement type="set_environment">JAVA_JAR_PATH</requirement> - <requirement type="set_environment">SNPEFF_JAR_PATH</requirement> - - <requirement type="set_environment">JAR_PATH1</requirement> - <requirement type="set_environment">JAR_PATH2</requirement> - --> - <requirement type="set_environment">TOOL_DIR</requirement> - - </requirements> - - <description>FALCO: Amplicon Analysis Pipeline</description> - - <!-- command block to call script with specific R installation (set full paths) --> - <!-- - <command> - /full/path/to/Rscript - /full/path/to/QDNAseq.R - $qdnaseq_cfg - </command> - --> - - <!-- command block to call script with default R environment --> - <command interpreter="bash"> - <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &&; echo "ECHO PRINT"; --> - <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; --> - falco-report.sh $falco_cfg; - </command> - <!-- - <command interpreter="bash"> - falco/amplicon-VcAn-TSACP.sh $bam $bam.name; - echo "DONE" - </command> - <command interpreter="perl"> - falco.pl $htmlFile ${htmlFile.files_path} $bam $bam.name; - </command> - --> - - <stdio> - <!-- Anything higher than 0 means the bash script didnt finish --> - <exit_code range="1:" level="fatal" description="Bash script didnt finish correctly, check log" /> - </stdio> - - <inputs> - <!-- ==================== --> - <!-- General inputs --> - <!-- ==================== --> - <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST"> - <validator type="empty_field" /> - <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator> - </param> - <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" /> - - <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/> - <param format="bed" name="design_file" optional="True" type="data" label="BED File" help="When left empty, default Cancer Panel is used"/> - <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/> - - <!-- ==================== --> - <!-- Option to use your own bin annotations --> - <!-- ==================== --> - - </inputs> - - <!-- ==================== --> - <!-- This config is sourced by tool --> - <!-- ==================== --> - <configfiles> - <configfile name="falco_cfg"> - design_file=$design_file - manifest_file=$manifest_file - bam_file=$bam - bam_name=$bam.name - <!--html_out=$html_output--> - vcf_out=$vcf_output - out_path=${vcf_output.files_path} - </configfile> - </configfiles> - <!-- - jar_path1=$JAR_PATH1 - jar_path2=$JAR_PATH2 - jar_path3=$JAVA_JAR_PATH - jar_path4=$SNPEFF_JAR_PATH - --> - <!-- ==================== --> - <!-- Main output is an html based report, additional on request --> - <!-- ==================== --> - <outputs> - <!--<data format="html" name="html_output" label="FALCO AAP (${jobName})" />--> - <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" /> - </outputs> - - <!-- ==================== --> - <!-- Tests still to be done --> - <!-- ==================== --> - - <!-- - <tests> - <test> - <param name="input1" value="input1" /> - <param name="input2" value="input2" /> - </test> - </tests> - --> - - <help> -.. class:: infomark - -**Introduction** - -This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_ - -.. _FALCO: https://bitbucket.org/daoud/falco - -Calls and annotates genomic variants for each amplicon in a design. - ------ - -**Citation** - -For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). - - </help> - -</tool>
--- a/falco/README Fri Oct 10 11:28:57 2014 -0400 +++ b/falco/README Tue Dec 23 11:26:33 2014 -0500 @@ -1,31 +1,24 @@ -# -# Author Daoud Sie -# e-mail d.sie@vumc.nl -# -###### +Usage: + +falco + +input: -Let's put some useful stuff here... - -The Amplicon Analysis Pipeline (AAP) takes fastq files as a starting point. However, each -stage of the pipeline can be run separately. - -amplicon-Al-TSACP.sh R1.fq R2.fq output - -This will run the following: +- bam file +- manifest file +- ref + fai +- locifilt +- manifest -- flash read merging -- adapter clipping -- quality trimmer -- alignemt using BWA +output: -- amplicon-VcAn-TSACP.sh --- variant calling and annotation: --- samtools variant caller --- custom variant caller --- snpEff effect prediction --- dbSNP annotations +- *.vcf file +- *.qc.ann.txt -> catalog of each assayed bp +- *.qc2.ann.txt -> catalog of transitions +- *.qc.targets.txt -> amplicon centered information, eg depth, start/end positions. -- amplicon-Report.sh --- filtering of variants --- report generation +example: +falco --bam input.bam --output outputBase --ref [hg19.fa] + +
--- a/falco/amplicon-Al-TSACP.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -source $DIR/init.sh - -TMP=./tmp -if [ ! -e $TMP ] -then - mkdir $TMP -fi - -fq1=$1 -fq2=$2 -output=$3 - -bfq1=`basename $fq1` -bfq2=`basename $fq2` - -if [ ! -e $TMP/$bfq1.trim ] -then -echo `date` " [$$] - $adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim" -$adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq1.qtrim ] -then -echo `date` " [$$] - $qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34" -$qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34 -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq2.trim ] -then -echo `date` " [$$] - $adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim" -$adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq2.qtrim ] -then -echo `date` " [$$] - $qTrim -t10 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34" -$qTrim -t30 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34 -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq1.qtrim.paired ] -then -echo `date` " [$$] - perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim" -perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim -echo `date` " [$$] - Done!" -fi - -# FLASH Fastq joiner -if [ ! -e $TMP/$output.flashed.fq ] -then - -$flash -r150 -f180 -c $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired > $TMP/$output.flashed.fq - -fi - -#if [ ! -e $TMP/$output ] -#then -#echo `date` " [$$] - $stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions=\"$bwaref\" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired" -#$stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions="$bwaref" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired -#echo `date` " [$$] - Done!" -#fi - -# Added -e 40 for maximum indel size of 40,... -#if [ ! -e $TMP/$output ] -#then -#echo `date` " [$$] - $stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions=\"-e 40 $bwaref\" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$output.flashed.fq" -#$stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions="-e 40 $bwaref" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$output.flashed.fq -#echo `date` " [$$] - Done!" -#fi - -if [ ! -e $output.bam ] -then -echo `date` " [$$] - $bwa aln -e 40 $bwaref $TMP/$output.flashed.fq > $TMP/$output.sai" -$bwa aln -e 40 $bwaref $TMP/$output.flashed.fq > $TMP/$output.sai -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $bwa samse -r \"@RG\\tID:$output\\tSM:$output\" $bwaref $TMP/$output.sai $TMP/$output.flashed.fq > $TMP/$output.sam" -$bwa samse -r "@RG\tID:$output\tSM:$output" $bwaref $TMP/$output.sai $TMP/$output.flashed.fq > $TMP/$output.sam -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $samtools view -uS $TMP/$output.sam | $samtools sort - $output" -$samtools view -uS $TMP/$output.sam | $samtools sort - $output -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $samtools index $output.bam" -$samtools index $output.bam -echo `date` " [$$] - Done!" -fi - -echo `date` "[$$] - $VcAn $output.bam $output" -$VcAn $output.bam $output -echo `date` "[$$] - Done!" - -echo `date` "[$$] - $report $output" -$report $output -echo `date` "[$$] - Done!" - -exit
--- a/falco/amplicon-AlVcAn-HaloPlex.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ -#!/bin/bash - -index=/scratch/data/ref/hg19/stampy/hg19 -hash=/scratch/data/ref/hg19/stampy/hg19 -bwaref=/scratch/data/ref/hg19/bwa-5/hg19.fa - -adapt_clipper=/opt/cutadapt/cutadapt-1.1/bin/cutadapt -illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" -illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" -qTrim=/opt/bin/fastq_quality_trimmer -pairUp=/storage/shark1/data/Git/ampliconPipeLine/pairUp.pl -stampy=/opt/stampy/stampy-1.0.18/stampy.py -samtools=/opt/samtools/samtools-0.1.18/samtools -pileup2cov=/storage/shark1/data/Git/ampliconPipeLine/pileup2cov.pl -attachManifest=/storage/shark1/data/Git/ampliconPipeLine/attachGff.pl -manifest=/scratch/data/ref/manifests/HaloPlex/Analyzable-region-01355-1335878719.gff -snpEff=/opt/snpEff/snpEff_3_0a - -plots=/storage/shark1/data/Git/ampliconPipeLine/plots.R - -fq1=$1 -fq2=$2 -output=$3 - -if [ ! -e $fq1.trim ] -then -echo `date` " [$$] - $adapt_clipper -a $illmP5 $fq1 > $fq1.trim" -$adapt_clipper -a $illmP5 $fq1 > $fq1.trim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $fq1.qtrim ] -then -echo `date` " [$$] - $qTrim -t30 -i $fq1.trim -o $fq1.qtrim -Q34" -$qTrim -t30 -i $fq1.trim -o $fq1.qtrim -Q34 -echo `date` " [$$] - Done!" -fi - -if [ ! -e $fq2.trim ] -then -echo `date` " [$$] - $adapt_clipper -a $illmP7 $fq2 > $fq2.trim" -$adapt_clipper -a $illmP7 $fq2 > $fq2.trim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $fq2.qtrim ] -then -echo `date` " [$$] - $qTrim -t30 -i $fq2.trim -o $fq2.qtrim -Q34" -$qTrim -t30 -i $fq2.trim -o $fq2.qtrim -Q34 -echo `date` " [$$] - Done!" -fi - -if [ ! -e $fq1.qtrim.paired ] -then -echo `date` " [$$] - perl $pairUp $fq1.qtrim $fq2.qtrim" -perl $pairUp $fq1.qtrim $fq2.qtrim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output ] -then -echo `date` " [$$] - $stampy -g $index -h $hash --bwaoptions=\"$bwaref\" -o $output -M $fq1.qtrim.paired $fq2.qtrim.paired" -$stampy -g $index -h $hash --bwaoptions="$bwaref" -o $output -M $fq1.qtrim.paired $fq2.qtrim.paired -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.bam ] -then -echo `date` " [$$] - $samtools view -uS $output | $samtools sort - $output" -$samtools view -uS $output | $samtools sort - $output -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $samtools index $output.bam" -$samtools index $output.bam -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.vcf ] -then -echo `date` " [$$] - $samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -F 0.01 -m 10 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf" -$samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -F 0.01 -m 10 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf -echo `date` " [$$] - Done!" -echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" -bcftools view $output.bcf > $output.vcf -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.txt ] -then -echo `date` " [$$] - java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o txt -c $snpEff/snpEff.config $output.vcf > $output.snpeff.vcf" -java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o txt -c $snpEff/snpEff.config $output.vcf > $output.snpeff.vcf -echo `date` " [$$] - Done!" - -dbSnp=/scratch/data/ref/dbSNP/dbSnp_120616.vcf -dbNSFP=/scratch/data/ref/dbNSFP/dbNSFP2.0b3.txt -snpSift=/opt/SnpSift - -echo `date` " [$$] [$$] - java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -echo `date` " [$$] [$$] - Done!" - -echo `date` " [$$] [$$] - java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -echo `date` " [$$] [$$] - Done!" - -fi - -if [ ! -e $output.qc.txt ] -then -echo `date` " [$$] - $pileup2cov $bwaref $output.bam > $output.qc.txt" -$samtools view -Xq10 $output.bam | $pileup2cov $bwaref > $output.qc.txt -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.qc.ann.txt ] -then -echo `date` " [$$] - $attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt" -$attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.pdf ] -then -echo `date` " [$$] - $plots $output.qc.ann.targets.txt $output.qc.targets.txt" -$plots $output.qc.ann.txt $output.qc.targets.txt $output.pdf -echo `date` " [$$] - Done!" -fi
--- a/falco/amplicon-AlVcAn-TSACP.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -TMP=./tmp -if [ ! -e $TMP ] -then - mkdir $TMP -fi - -index=$DIR/ref/hg19/stampy/hg19 -hash=$DIR/ref/hg19/stampy/hg19 -bwaref=$DIR/ref/hg19/bwa-5/hg19.fa -manifest=$DIR/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt - -illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" -illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" - -adapt_clipper=$DIR/bin/cutadapt/cutadapt-1.1/bin/cutadapt -qTrim=$DIR/bin/fastq_quality_trimmer -stampy=$DIR/bin/stampy/stampy-1.0.18/stampy.py -samtools=$DIR/bin/samtools/samtools-0.1.18/samtools -snpEff=$DIR/bin/snpEff/snpEff_3_0a -varscan=$DIR/bin/VarScan/VarScan.v2.2.11.jar -java=/usr/java/latest/bin/java -bwa=$DIR/bin/bwa/bwa-0.5.9/bwa - -pairUp=$DIR/misc/pairUp.pl -pileup2cov=$DIR/misc/pileup2cov.pl -attachManifest=$DIR/misc/attachManifest.pl -plots=$DIR/misc/plots.R -VcAn=$DIR/amplicon-VcAn-TSACP.sh -report=$DIR/amplicon-Report.sh - -fq1=$1 -fq2=$2 -output=$3 - -bfq1=`basename $fq1` -bfq2=`basename $fq2` - -if [ ! -e $TMP/$bfq1.trim ] -then -echo `date` " [$$] - $adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim" -$adapt_clipper -a $illmP5 $fq1 > $TMP/$bfq1.trim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq1.qtrim ] -then -echo `date` " [$$] - $qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34" -$qTrim -t30 -i $TMP/$bfq1.trim -o $TMP/$bfq1.qtrim -Q34 -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq2.trim ] -then -echo `date` " [$$] - $adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim" -$adapt_clipper -a $illmP7 $fq2 > $TMP/$bfq2.trim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq2.qtrim ] -then -echo `date` " [$$] - $qTrim -t10 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34" -$qTrim -t30 -i $TMP/$bfq2.trim -o $TMP/$bfq2.qtrim -Q34 -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$bfq1.qtrim.paired ] -then -echo `date` " [$$] - perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim" -perl $pairUp $TMP/$bfq1.qtrim $TMP/$bfq2.qtrim -echo `date` " [$$] - Done!" -fi - -if [ ! -e $TMP/$output ] -then -echo `date` " [$$] - $stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions=\"$bwaref\" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired" -$stampy -g $index -h $hash --readgroup=ID:$output,SM:$output --gatkcigarworkaround --bwaoptions="$bwaref" --bwa="$bwa" --bwamark -o $TMP/$output -M $TMP/$bfq1.qtrim.paired $TMP/$bfq2.qtrim.paired -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.bam ] -then -echo `date` " [$$] - $samtools view -uS $TMP/$output | $samtools sort - $output" -$samtools view -uS $TMP/$output | $samtools sort - $output -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $samtools index $output.bam" -$samtools index $output.bam -echo `date` " [$$] - Done!" -fi - -echo `date` "[$$] - $VcAn $output.bam $output" -$VcAn $output.bam $output -echo `date` "[$$] - Done!" - -echo `date` "[$$] - $report $output" -$report $output -echo `date` "[$$] - Done!" - -exit -if [ ! -e $output.vcf ] -then -# Use Extended BAQ! -# Tweak indel settings -m and -F -echo `date` " [$$] - $samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf" -$samtools mpileup -Euf $bwaref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $output.bam | bcftools view -bvcg - > $output.bcf -echo `date` " [$$] - Done!" -echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" -bcftools view $output.bcf > $output.vcf -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.vs.snp.vcf ] -then -# VarScan seems a better alternative for smaller VAF's Samtools seems to obscure some false negatives.... -echo `date` " [$$] - $samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 --output-vcf > $output.vs.snp.vcf" -$samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 --output-vcf > $output.vs.snp.vcf -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.vs.snp.tsv ] -then -# VarScan seems a better alternative for smaller VAF's Samtools seems to obscure some false negatives.... -echo `date` " [$$] - $samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 > $output.vs.snp.tsv" -$samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2snp --min-var-freq 0.05 > $output.vs.snp.tsv -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.vs.indel.vcf ] -then -echo `date` " [$$] - $samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2indel --min-var-freq 0.05 --output-vcf > $output.vs.indel.vcf" -$samtools mpileup -Bf $bwaref $output.bam | $java -jar $varscan mpileup2indel --min-var-freq 0.05 --output-vcf > $output.vs.indel.vcf -echo `date` " [$$] - Done!" -fi - -# Annotation -dbSnp=/scratch/data/ref/dbSNP/dbSnp_120616.vcf -dbNSFP=/scratch/data/ref/dbNSFP/dbNSFP2.0b3.txt -snpSift=/opt/SnpSift - -VcfIn=$output.vcf -VcfOut=$output.samtools.vcf - -if [ ! -e $VcfOut ] -then -# Samtools annotation -echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -mv $output.snpeff.vcf $VcfOut -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -echo `date` " [$$] - Done!" -fi - -VcfIn=$output.vs.snp.vcf -VcfOut=$output.vs.snp.a.vcf - -if [ ! -e $VcfOut ] -then -# VarScan SNP annotation -echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -mv $output.snpeff.vcf $VcfOut -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -echo `date` " [$$] - Done!" -fi - -VcfIn=$output.vs.indel.vcf -VcfOut=$output.vs.indel.a.vcf - -if [ ! -e $VcfOut ] -then -# VarScan INDEL annotation -echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -mv $output.snpeff.vcf $VcfOut -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -echo `date` " [$$] - Done!" -fi - - -if [ ! -e $output.qc.txt ] -then -echo `date` " [$$] - $pileup2cov $bwaref $output.bam > $output.qc.txt" -$samtools view -Xq10 $output.bam | $pileup2cov $bwaref > $output.qc.txt -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $samtools view -Xq10 -f0x0040 $output.bam | $pileup2cov $bwaref $output.bam > $output.R1.qc.txt" -$samtools view -Xq10 -f0x0040 $output.bam | $pileup2cov $bwaref > $output.R1.qc.txt -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $samtools view -Xq10 -f0x0080 $output.bam | $pileup2cov $bwaref $output.bam > $output.R2.qc.txt" -$samtools view -Xq10 -f0x0080 $output.bam | $pileup2cov $bwaref > $output.R2.qc.txt -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt" -$attachManifest $manifest $output.qc.txt $output.qc.targets.txt > $output.qc.ann.txt -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $attachManifest $manifest $output.R1.qc.txt $output.R1.qc.targets.txt > $output.R1.qc.ann.txt" -$attachManifest $manifest $output.R1.qc.txt $output.R1.qc.targets.txt > $output.R1.qc.ann.txt -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $attachManifest $manifest $output.R2.qc.txt $output.R2.qc.targets.txt > $output.R2.qc.ann.txt" -$attachManifest $manifest $output.R2.qc.txt $output.R2.qc.targets.txt > $output.R2.qc.ann.txt -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $plots $output.qc.ann.targets.txt $output.qc.targets.txt" -$plots $output.qc.ann.txt $output.qc.targets.txt $output.pdf -echo `date` " [$$] - Done!" -fi
--- a/falco/amplicon-QC.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -#!/bin/bash - -bam=$1 -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -TMP=./tmp -if [ ! -e $TMP ] -then - mkdir $TMP -fi - -source $DIR/init.sh - -#targetBed=$DIR/ref/manifests/TSACP/TSACP.bed -#samtools=$DIR/bin/samtools/samtools-0.1.18/samtools -#alignmentStats=$DIR/misc/alignmentStats.pl -#errorRate=$DIR/misc/errorRate.pl -#plotQc=$DIR/misc/plotsQC.R - -#export PATH=$PATH:$DIR/bin/samtools/samtools-0.1.18/ - -if [ ! -e alignmentStats.tsv ] -then -$alignmentStats $targetBed $bam > alignmentStats.tsv -fi - -if [ ! -e errorStats.tsv ] -then -$errorRate *.qc.ann.txt > errorStats.tsv -fi - -Rscript $plotQc alignmentStats.tsv errorStats.tsv - -
--- a/falco/amplicon-Report.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -source $DIR/init.sh - - -base=$1 - -vcf2tsv=$DIR/misc/vcf2tsv.pl -spliteff=$DIR/misc/splitEff.pl -addQc=$DIR/misc/addQc.pl -filterR=$DIR/misc/filter.R -filter=$DIR/misc/filter.pl -plotPng=$DIR/misc/plotsPng.R - -# convert to tsv - -echo `date` " [$$] - converting vcf to tsv" -$vcf2tsv $base.samtools.vcf > $base.samtools.tsv -#$vcf2tsv $base.vs.snp.a.vcf > $base.vs.snp.a.tsv -$vcf2tsv $base.qc.ann.filt.a.vcf > $base.qc.ann.filt.a.tsv -$vcf2tsv $base.qc.ann.clinvar.a.vcf > $base.qc.ann.clinvar.a.tsv -#$vcf2tsv $base.qc.ann.2.a.vcf > $base.qc.ann.2.a.tsv - -# split eff columns -echo `date` " [$$] - splitting vcf columns" -$spliteff $base.samtools.tsv Samtools > $base.res.tsv -#$spliteff $base.vs.snp.a.tsv >> $base.res.tsv -$spliteff $base.qc.ann.filt.a.tsv Custom >> $base.res.tsv -$spliteff $base.qc.ann.clinvar.a.tsv Clinvar >> $base.res.tsv -#$spliteff $base.qc.ann.2.a.tsv Custom2 >> $base.res.tsv - -# add count data -#$addQc $base.res.tmp $base.qc.ann.txt > $base.res.tsv - -# Filter -echo `date` " [$$] - filtering data" -#Rscript $filterR $base.res.tsv $base.qc.ann.txt 10 100 .95 $base -$filter $base.res.tsv $canonicals > $base.res.filtered.tsv - -# Plot -echo `date` " [$$] - plotting data" -Rscript $plotPng $base.qc.ann.qual.txt $base.qc2.ann.txt $base.qc.targets.txt $base.res.filtered.tsv $base.qc.ann.qual.clinvar.txt $locifilt $base
--- a/falco/amplicon-VcAn-TSACP.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -#!/bin/bash -echo `date` " [$$] - Starting now in amplicon-VcAn-TSACP.sh!" - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -source $DIR/init.sh - -TMP=./tmp -if [ ! -e $TMP ] -then - mkdir $TMP -fi - -bam=$1 -output=$2 - -if [ ! -e $output.vcf ] -then -# Use Extended BAQ! -# Tweak indel settings -m and -F -echo `date` " [$$] - $samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | bcftools view -bvcg - > $output.bcf" -$samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | $bcftools view -bvcg - > $output.bcf -echo `date` " [$$] - Done!" -echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" -$bcftools view $output.bcf > $output.vcf -echo `date` " [$$] - Done!" -fi - -# Annotation -#VcfIn=$output.vcf -#VcfOut=$output.samtools.vcf - -#if [ ! -e $VcfOut ] -#then -# Samtools annotation -#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -#mv $output.snpeff.2.vcf $VcfOut -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -#echo `date` " [$$] - Done!" -#fi - -if [ ! -e $output.qc.ann.txt ] -then -echo `date` " [$$] - $pileup2cov2 $bam $faref $manifest $output $samtools" -$pileup2cov2 $bam $faref $manifest $output $samtools -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.qc.ann.qual.txt ] -then -echo `date` " [$$] - RScript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt" -Rscript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt -echo `date` " [$$] - Done!" -fi - -echo `date` " [$$] - $qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output" -$qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf" -$qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf" -$qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf -echo `date` " [$$] - Done!" - - - -#VcfIn=$output.qc.ann.filt.vcf -#VcfOut=$output.qc.ann.filt.a.vcf - -#if [ ! -e $VcfOut ] -#then - -# qc vcf annotation -#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -#mv $output.snpeff.2.vcf $VcfOut -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -#echo `date` " [$$] - Done!" -#fi - -#VcfIn=$output.qc.ann.clinvar.vcf -# VcfOut=$output.qc.ann.clinvar.a.vcf - -#if [ ! -e $VcfOut ] -#then - -# qc vcf annotation -#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -#mv $output.snpeff.2.vcf $VcfOut -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -#echo `date` " [$$] - Done!" -#fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/bin/falco Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,69 @@ +#!/usr/bin/perl + +use strict; +use Cwd 'abs_path'; +use Getopt::Long; +use File::Basename; + +my $absPath = abs_path($0); +my $dn = dirname($absPath); + +# Set options + +my $bam; +my $ref = "$dn/../ref/hg19/hg19.fa"; +my $locifilt = "$dn/../ref/filters/filter.tsv"; +my $manifest = "$dn/../ref/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; +my $base = $bam; + +GetOptions ( + "bam=s" => \$bam, + "ref=s" => \$ref, + "filter=s" => \$locifilt, + "manifest=s" => \$manifest, + "output=s" => \$base, + ) +or die("Error in command line arguments\n"); + +# Set paths to external script +# TODO make modules + +my $perAmpliconAnalysis = "$dn/../lib/perl/perAmpliconAnalysis.pl"; +my $addQual = "$dn/../lib/R/addQual.R"; +my $func = "$dn/../lib/R/func.R"; +my $qcFilt = "$dn/../lib/perl/qcFilt.pl"; +my $qc2vcf = "$dn/../lib/perl/qc2vcf.pl"; + +# Check Rscript +my $rscript = `which Rscript`; +chomp $rscript; +if ($rscript !~ /Rscript$/) { + print STDERR "No Rscript present in PATH\n"; + exit 1; +} + +# Check samtools +my $samtools = `which samtools`; +chomp $samtools; +if ($samtools !~ /samtools$/) { + print STDERR "No samtools present in PATH\n"; + exit 1; +} + +# perl perAmpliconAnalysis +# R addQual.R +# perl qcFilt +# perl qc2vcf + +print STDOUT localtime() . " [$$] $perAmpliconAnalysis $bam $ref $manifest $base $samtools\n"; +system("$perAmpliconAnalysis $bam $ref $manifest $base $samtools"); + +print STDOUT localtime() . " [$$] $rscript $addQual $base.qc.ann.txt $base.qc.ann.qual.txt $func $locifilt\n"; +system("$rscript $addQual $base.qc.ann.txt $base.qc.ann.qual.txt $func $locifilt"); + +print STDOUT localtime() . " [$$] $qcFilt $base.qc.ann.qual.txt $base\n"; +system("$qcFilt $base.qc.ann.qual.txt $base"); + +print STDOUT localtime() . " [$$] $qc2vcf $base.qc.ann.qual.filt.txt > $base.falco.vcf\n"; +system("$qc2vcf $base.qc.ann.qual.filt.txt > $base.falco.vcf"); +
--- a/falco/init.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -index=/ccagc/data/ref/hg19/stampy/hg19 -hash=/ccagc/data/ref/hg19/stampy/hg19 -faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa -#manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt -#targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed - -dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf -dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt -clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf -cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf -cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf -locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv -canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv - -illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" -illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" - -adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt -qTrim=/ccagc/bin/fastq_quality_trimmer -stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py -#samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools -#bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools -snpEff=/ccagc/lib/snpEff/snpEff_3_0a -snpEff=/ccagc/lib/snpEff/snpEff_v3_4 -snpSift=/ccagc/lib/SnpSift - -varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar -java=/usr/bin/java -bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa -flash=/ccagc/lib/flash/FLASH-1.2.2/flash - -pairUp=$DIR/misc/pairUp.pl -pileup2cov=$DIR/misc/pileup2cov.pl -pileup2cov2=$DIR/misc/perAmpliconAnalysis.pl -addQual=$DIR/misc/addQual.R - -qc2vcf=$DIR/misc/qc2vcf.pl -qcFilt=$DIR/misc/qcFilt.pl -plots=$DIR/misc/plots.R -plotsPng=$DIR/misc/plotsPng.R - -attachManifest=$DIR/misc/attachManifest.pl -plots=$DIR/misc/plots.R -VcAn=$DIR/amplicon-VcAn-TSACP.sh -report=$DIR/amplicon-Report.sh - -alignmentStats=$DIR/misc/alignmentStats.pl -errorRate=$DIR/misc/errorRate.pl -plotQc=$DIR/misc/plotsQC.R - -#export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/ -source ./galaxy_init.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/lib/R/addQual.R Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,21 @@ +#!/usr/bin/Rscript +args <- commandArgs(T) +qcFile <- args[1] +output <- args[2] +funcR <- args[3] +lociFiltFile <- args[4] + +read.delim(lociFiltFile, header=F) -> lociFiltD +lociFilt <- paste(paste("chr", lociFiltD[,1], sep=""), lociFiltD[,2], sep=":") + +source(funcR) +read.delim(qcFile, header=T) -> qc + +#addQual(qc) -> qc.qual +addQualTransCor(qc, lociFilt) -> qc.qual +#addQualVarCor(qc) -> qc.qual + +write.table(qc.qual, output, row.names=F, col.names=T, quote=F, sep="\t") +#write.table(qc[selection,], output, row.names=F, col.names=T, quote=F, sep="\t") + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/lib/R/func.R Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,575 @@ +#!/usr/bin/Rscript +#args <- commandArgs(T) +#qcFile <- args[1] +#output <- args[2] + +#read.delim(qcFile, header=T) -> qc + +addQual <- function(qc) { + +qc$del <- as.character(as.vector(qc$del)) +qc$ins <- as.vector(qc$ins) +qc$pVal <- 1 +qc$pValAdj <- 1 +#qc$pValPois <- 1 +qc$qScore <- 0 +qc$qScoreI <- 0 +qc$qScoreD <- 0 + +pVal.I <- rep(1, nrow(qc)) +pVal.D <- rep(1, nrow(qc)) + +delSel <- qc$del != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[delSel]), "\\|")), ":")), ncol=2, byrow=T)) -> dels +dels$ln <- nchar(as.vector(dels$X1)) +colnames(dels) <- c("seq", "occ", "ln") +delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +insSel <- qc$ins != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[insSel]), "\\|")), ":")), ncol=2, byrow=T)) -> inss +inss$ln <- nchar(as.vector(inss$X1)) +colnames(inss) <- c("seq", "occ", "ln") +insPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +# Calculate errorrate per amplicon +amps <- unique(qc$amp) +for (i in amps) { + #print(i) + sel <- qc$amp == i + prob <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) + #prob <- median(qc$nVar[sel] / (qc$nRef[sel] + qc$nVar[sel])) + pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob, lower.tail=F) + qc$pVal[sel] <- pees +# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) +# qc$pValPois[sel] <- pois + + # Seperate for indel/deletion events + selDels <- delSel & sel + if (sum(selDels) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 + dels2$ln <- nchar(as.vector(dels2$X1)) + colnames(dels2) <- c("seq", "occ", "ln") + dels2$occ <- as.numeric(as.vector(dels2$occ)) + } + for (j in which(selDels)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels + dels$ln <- nchar(as.vector(dels$X1)) + colnames(dels) <- c("seq", "occ", "ln") + dels$occ <- as.numeric(as.vector(dels$occ)) + #dels$pDel <- delPees[as.integer(dels$ln)] + #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) + dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) + dels$Q <- -10 * log10(dels$pVal) + + high <- order(dels$occ, -dels$Q, decreasing=T)[1] + qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") + qc$qScoreD[j] <- dels$Q[high] + pVal.D[j] <- dels$pVal[high] + } + selIns <- insSel & sel + if (sum(selIns) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 + inss2$ln <- nchar(as.vector(inss2$X1)) + colnames(inss2) <- c("seq", "occ", "ln") + inss2$occ <- as.numeric(as.vector(inss2$occ)) + } + for (j in which(selIns)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss + inss$ln <- nchar(as.vector(inss$X1)) + colnames(inss) <- c("seq", "occ", "ln") + inss$occ <- as.numeric(as.vector(inss$occ)) + #inss$pIns <- insPees[as.integer(inss$ln)] + #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) + inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) + inss$Q <- -10 * log10(inss$pVal) + + high <- order(inss$occ, -inss$Q, decreasing=T)[1] + qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") + qc$qScoreI[j] <- inss$Q[high] + pVal.I[j] <- inss$pVal[high] + } + #print(sum(-10 * log10(pees) > 100)) + #print(sum(qc$qScoreI[selIns] > 100)) + #print(sum(qc$qScoreD[selDels] > 100)) +} + +p.adjust(qc$pVal) -> qc$pValAdj +-10 * log(p.adjust(pVal.I)) -> qc$qScoreI +-10 * log(p.adjust(pVal.D)) -> qc$qScoreD +qc$qScore <- -10 * log10(qc$pValAdj) +#qc$qScore[qc$pValAdj == 0] <- 1000 +qc$qScore[qc$qScore > 1000] <- 1000 +qc$qScoreI[qc$qScoreI > 1000] <- 1000 +qc$qScoreD[qc$qScoreD > 1000] <- 1000 +qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) +dpfilt <- as.numeric(qc$dp) >= 100 +#varfilt <- as.numeric(qc$nVar) >= 10 + +selection <- qsel & dpfilt + +print(paste("Filtered out: ", sum(!selection), sep="")) +print(paste("Variants selected: ", sum(selection), sep="")) +return(qc) +} + +addQualTransCor <- function(qc, lociFilt) { + + +# lociFilt contains snp, cosmic and clinvar positions + +qc$del <- as.character(as.vector(qc$del)) +#qc$del <- as.character(as.vector(qc$del)) +qc$ins <- as.character(as.vector(qc$ins)) +qc$pVal <- 1 +qc$pValAdj <- 1 +#qc$pValPois <- 1 +qc$qScore <- 0 +qc$qScoreI <- 0 +qc$qScoreD <- 0 + +pVal.I <- rep(1, nrow(qc)) +pVal.D <- rep(1, nrow(qc)) + +rle(as.vector(qc$ntRef)) -> srle +hompols <- srle$lengths >= 5 +homPosS <- cumsum(srle$lengths)[hompols] +homPosE <- cumsum(srle$lengths)[which(hompols) - 1] +homFilt <- rep(F, nrow(qc)) +homFilt[homPosS] <- T +homFilt[homPosE] <- T + +delSel <- qc$del != "." & !homFilt +if (sum(delSel > 0)) { + + +data.frame(matrix(unlist(strsplit(unlist(strsplit(qc$del[delSel], "\\|")), ":")), ncol=2, byrow=T)) -> dels +dels$ln <- nchar(as.vector(dels$X1)) +colnames(dels) <- c("seq", "occ", "ln") +delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) +} + +insSel <- qc$ins != "." & !homFilt +if (sum(insSel) > 0) { +data.frame(matrix(unlist(strsplit(unlist(strsplit(qc$ins[insSel], "\\|")), ":")), ncol=2, byrow=T)) -> inss +inss$ln <- nchar(as.vector(inss$X1)) +colnames(inss) <- c("seq", "occ", "ln") +insPees <- ppois(1:50, mean(rep(inss$ln, inss$occ)), lower.tail=F) +} +# Calculate transition bias + + +#calcTransCor(qc) -> pCor +globalProb <- sum(qc$nVar) / (sum(qc$nRef) + sum(qc$nVar)) +# Calculate errorrate per amplicon +amps <- unique(qc$amp) +for (i in amps) { + #print(i) + sel <- qc$amp == i + prob1 <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) + prob <- prob1 * calcTransCor(qc[sel,], lociFilt) + pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob , lower.tail=F) + qc$pVal[sel] <- pees +# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) +# qc$pValPois[sel] <- pois + + # Seperate for indel/deletion events + selDels <- delSel & sel + if (sum(selDels) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 + dels2$ln <- nchar(as.vector(dels2$X1)) + colnames(dels2) <- c("seq", "occ", "ln") + dels2$occ <- as.numeric(as.vector(dels2$occ)) + + for (j in which(selDels)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels + dels$ln <- nchar(as.vector(dels$X1)) + colnames(dels) <- c("seq", "occ", "ln") + dels$occ <- as.numeric(as.vector(dels$occ)) + #dels$pDel <- delPees[as.integer(dels$ln)] + #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) + dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) + dels$Q <- -10 * log10(dels$pVal) + + high <- order(dels$occ, -dels$Q, decreasing=T)[1] + qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") + qc$qScoreD[j] <- dels$Q[high] + pVal.D[j] <- dels$pVal[high] + } + } + selIns <- insSel & sel + if (sum(selIns) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 + inss2$ln <- nchar(as.vector(inss2$X1)) + colnames(inss2) <- c("seq", "occ", "ln") + inss2$occ <- as.numeric(as.vector(inss2$occ)) + + for (j in which(selIns)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss + inss$ln <- nchar(as.vector(inss$X1)) + colnames(inss) <- c("seq", "occ", "ln") + inss$occ <- as.numeric(as.vector(inss$occ)) + #inss$pIns <- insPees[as.integer(inss$ln)] + #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) + inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) + inss$Q <- -10 * log10(inss$pVal) + + high <- order(inss$occ, -inss$Q, decreasing=T)[1] + qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") + qc$qScoreI[j] <- inss$Q[high] + pVal.I[j] <- inss$pVal[high] +} } + #print(sum(-10 * log10(pees) > 100)) + #print(sum(qc$qScoreI[selIns] > 100)) + #print(sum(qc$qScoreD[selDels] > 100)) +} + +p.adjust(qc$pVal) -> qc$pValAdj +-10 * log(p.adjust(pVal.I)) -> qc$qScoreI +-10 * log(p.adjust(pVal.D)) -> qc$qScoreD +qc$qScore <- -10 * log10(qc$pValAdj) +#qc$qScore[qc$pValAdj == 0] <- 1000 +qc$qScore[qc$qScore > 1000] <- 1000 +qc$qScoreI[qc$qScoreI > 1000] <- 1000 +qc$qScoreD[qc$qScoreD > 1000] <- 1000 +qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) +dpfilt <- as.numeric(qc$dp) >= 100 +#varfilt <- as.numeric(qc$nVar) >= 10 + +selection <- qsel & dpfilt + +print(paste("Filtered out: ", sum(!selection), sep="")) +print(paste("Variants selected: ", sum(selection), sep="")) +return(qc) +} + + +addQualVarCor <- function(qc) { +# Corrected for variant occurence + +qc$del <- as.character(as.vector(qc$del)) +qc$ins <- as.vector(qc$ins) +qc$pVal <- 1 +qc$pValAdj <- 1 +#qc$pValPois <- 1 +qc$qScore <- 0 +qc$qScoreI <- 0 +qc$qScoreD <- 0 + +pVal.I <- rep(1, nrow(qc)) +pVal.D <- rep(1, nrow(qc)) + +delSel <- qc$del != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[delSel]), "\\|")), ":")), ncol=2, byrow=T)) -> dels +dels$ln <- nchar(as.vector(dels$X1)) +colnames(dels) <- c("seq", "occ", "ln") +delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +insSel <- qc$ins != "." +data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[insSel]), "\\|")), ":")), ncol=2, byrow=T)) -> inss +inss$ln <- nchar(as.vector(inss$X1)) +colnames(inss) <- c("seq", "occ", "ln") +insPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) + +# Calculate base bias per run +sum(qc$nA[grepl("A", qc$ntRef, ignore.case=T)]) -> refA +sum(qc$nA[!grepl("A", qc$ntRef, ignore.case=T)]) -> varA +sum(qc$nC[grepl("C", qc$ntRef, ignore.case=T)]) -> refC +sum(qc$nC[!grepl("C", qc$ntRef, ignore.case=T)]) ->varC +sum(qc$nG[grepl("G", qc$ntRef, ignore.case=T)]) -> refG +sum(qc$nG[!grepl("G", qc$ntRef, ignore.case=T)]) -> varG +sum(qc$nT[grepl("T", qc$ntRef, ignore.case=T)]) -> refT +sum(qc$nT[!grepl("T", qc$ntRef, ignore.case=T)]) -> varT + +varA / (refA + varA) -> errA +varC / (refC + varC) -> errC +varG / (refG + varG) -> errG +varT / (refT + varT) -> errT +c(errA, errC, errG, errT) / mean(c(errA, errC, errG, errT)) -> errACGT + +errMat <- qc[,9:12] +errMat[grepl("A", qc$ntRef, ignore.case=T),1] <- 0 +errMat[grepl("C", qc$ntRef, ignore.case=T),2] <- 0 +errMat[grepl("G", qc$ntRef, ignore.case=T),3] <- 0 +errMat[grepl("T", qc$ntRef, ignore.case=T),4] <- 0 + +pCor <- rep(1, nrow(qc)) +pCor[grepl("^A", qc$ntVar, ignore.case=T)] <- errACGT[1] +pCor[grepl("^C", qc$ntVar, ignore.case=T)] <- errACGT[2] +pCor[grepl("^G", qc$ntVar, ignore.case=T)] <- errACGT[3] +pCor[grepl("^T", qc$ntVar, ignore.case=T)] <- errACGT[4] + +# Calculate errorrate per amplicon +amps <- unique(qc$amp) +for (i in amps) { + #print(i) + sel <- qc$amp == i + prob <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) + #prob <- median(qc$nVar[sel] / (qc$nRef[sel] + qc$nVar[sel])) + pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob * pCor[sel], lower.tail=F) + qc$pVal[sel] <- pees +# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) +# qc$pValPois[sel] <- pois + + # Seperate for indel/deletion events + selDels <- delSel & sel + if (sum(selDels) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 + dels2$ln <- nchar(as.vector(dels2$X1)) + colnames(dels2) <- c("seq", "occ", "ln") + dels2$occ <- as.numeric(as.vector(dels2$occ)) + } + for (j in which(selDels)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels + dels$ln <- nchar(as.vector(dels$X1)) + colnames(dels) <- c("seq", "occ", "ln") + dels$occ <- as.numeric(as.vector(dels$occ)) + #dels$pDel <- delPees[as.integer(dels$ln)] + #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) + dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) + dels$Q <- -10 * log10(dels$pVal) + + high <- order(dels$occ, -dels$Q, decreasing=T)[1] + qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") + qc$qScoreD[j] <- dels$Q[high] + pVal.D[j] <- dels$pVal[high] + } + selIns <- insSel & sel + if (sum(selIns) > 0) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 + inss2$ln <- nchar(as.vector(inss2$X1)) + colnames(inss2) <- c("seq", "occ", "ln") + inss2$occ <- as.numeric(as.vector(inss2$occ)) + } + for (j in which(selIns)) { + data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss + inss$ln <- nchar(as.vector(inss$X1)) + colnames(inss) <- c("seq", "occ", "ln") + inss$occ <- as.numeric(as.vector(inss$occ)) + #inss$pIns <- insPees[as.integer(inss$ln)] + #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) + inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) + inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) + inss$Q <- -10 * log10(inss$pVal) + + high <- order(inss$occ, -inss$Q, decreasing=T)[1] + qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") + qc$qScoreI[j] <- inss$Q[high] + pVal.I[j] <- inss$pVal[high] + } + #print(sum(-10 * log10(pees) > 100)) + #print(sum(qc$qScoreI[selIns] > 100)) + #print(sum(qc$qScoreD[selDels] > 100)) +} + +p.adjust(qc$pVal) -> qc$pValAdj +-10 * log(p.adjust(pVal.I)) -> qc$qScoreI +-10 * log(p.adjust(pVal.D)) -> qc$qScoreD +qc$qScore <- -10 * log10(qc$pValAdj) +#qc$qScore[qc$pValAdj == 0] <- 1000 +qc$qScore[qc$qScore > 1000] <- 1000 +qc$qScoreI[qc$qScoreI > 1000] <- 1000 +qc$qScoreD[qc$qScoreD > 1000] <- 1000 +qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) +dpfilt <- as.numeric(qc$dp) >= 100 +#varfilt <- as.numeric(qc$nVar) >= 10 + +selection <- qsel & dpfilt + +print(paste("Filtered out: ", sum(!selection), sep="")) +print(paste("Variants selected: ", sum(selection), sep="")) +return(qc) +} + +#addQual(qc) -> qc +#write.table(qc, output, row.names=F, col.names=T, quote=F, sep="\t") +#write.table(qc[selection,], output, row.names=F, col.names=T, quote=F, sep="\t") + +calcTrans <- function(qcRaw, lociFilt = NULL) { + +sel <- rep(T, nrow(qcRaw)) +if (!is.null(lociFilt)) { +paste(qcRaw$X.chr, qcRaw$pos, sep=":") -> qcpos +sel <- ! qcpos %in% lociFilt +} + +qc <- qcRaw[sel,] + +# Calculate transition bias +refA <- grepl("A", qc$ntRef, ignore.case=T) +refC <- grepl("C", qc$ntRef, ignore.case=T) +refG <- grepl("G", qc$ntRef, ignore.case=T) +refT <- grepl("T", qc$ntRef, ignore.case=T) +varA <- grepl("A", qc$ntVar, ignore.case=T) +varC <- grepl("C", qc$ntVar, ignore.case=T) +varG <- grepl("G", qc$ntVar, ignore.case=T) +varT <- grepl("T", qc$ntVar, ignore.case=T) +varN <- grepl(".", qc$ntVar, ignore.case=T) +callA <- grepl("^A", qc$ntVar, ignore.case=T) +callC <- grepl("^C", qc$ntVar, ignore.case=T) +callG <- grepl("^G", qc$ntVar, ignore.case=T) +callT <- grepl("^T", qc$ntVar, ignore.case=T) +ntA <- sum(refA) +ntC <- sum(refC) +ntG <- sum(refG) +ntT <- sum(refT) + +callList <- list(callA, callC, callG, callT) +varList <- list(varA, varC, varG, varT) +refList <- list(refA, refC, refG, refT) + +#tots <- c( +#rep(sum(qc$nRef[refA], qc$nVar[refA]), 4), +#rep(sum(qc$nRef[refC], qc$nVar[refC]), 4), +#rep(sum(qc$nRef[refG], qc$nVar[refG]), 4), +#rep(sum(qc$nRef[refT], qc$nVar[refT]), 4)) + +nvar <- c( +rep(sum(qc$nC[refA], qc$nG[refA], qc$nT[refA]), 4), +rep(sum(qc$nA[refC], qc$nG[refC], qc$nT[refC]), 4), +rep(sum(qc$nA[refG], qc$nC[refG], qc$nT[refG]), 4), +rep(sum(qc$nA[refT], qc$nC[refT], qc$nG[refT]), 4)) + +ncall <- c( +rep(sum(qc$nVar[refA]), 4), +rep(sum(qc$nVar[refC]), 4), +rep(sum(qc$nVar[refG]), 4), +rep(sum(qc$nVar[refT]), 4)) + +nref <- c( +rep(sum(qc$nRef[refA]), 4), +rep(sum(qc$nRef[refC]), 4), +rep(sum(qc$nRef[refG]), 4), +rep(sum(qc$nRef[refT]), 4)) + +tots <- nref + nvar + +nts <- c("A", "C", "G", "T") +sumTrans <- data.frame(trans=paste(rep(nts, each=4), rep(nts, 4), sep=":"), npos=rep(c(ntA, ntC, ntG, ntT), each=4), cnt=rep(0, 16), tot=tots, nvar=nvar, nref=nref, ncall=ncall) + +for (i in 1:4) { + pos <- (i - 1) * 4 +for (j in 1:4) { +# print(sum(refList[[i]] & varList[[j]])) + + cnt <- sum(qc[refList[[i]] & varList[[j]], 8 + j]) + if (i == j) { +# cnt <- sum(qc[refList[[i]] & varN, 8 + j]) + cnt <- NA + } + sumTrans$cnt[pos + j] <- cnt + #print(cnt) +}} + +#sumTrans$cnt / sumTrans$nvar / sumTrans$tot * 1000000 -> tmp +sumTrans$cnt / sumTrans$tot * 1000000 -> tmp + +#totalNT <- sum(qc$nVar) + sum(qc$nRef) +#sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor +sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor +tmp / median(tmp, na.rm=T) -> sumTrans$cor2 + +sumTrans$cor[sumTrans$npos <= 15] <- 1 +sumTrans$cor2[sumTrans$npos <= 15] <- 1 + +#sumTrans$cnt / totalNT -> sumTrans$cor +#sumTrans$cnt / min(sumTrans$cnt, na.rm=T) -> sumTrans$cor + +return(sumTrans) + +} + +calcTransCor <- function(qcRaw, lociFilt = NULL) { + +calcTrans(qcRaw, lociFilt) -> sumTrans + +pCor <- rep(1, nrow(qcRaw)) +paste(qcRaw$ntRef, substr(qcRaw$ntVar, 1, 1), sep=":") -> qcTrans + +for (i in c("A", "C", "G", "T")) { +for (j in c("A", "C", "G", "T")) { + if (i != j) { + tTrans <- paste(i, j, sep=":") + pCor[grepl(tTrans, qcTrans, ignore.case=T)] <- sumTrans$cor2[sumTrans$trans == tTrans] + } + +}} +return(pCor) +} + + +calcTransCorOld <- function(qc) { +# Calculate transition bias +refA <- grepl("A", qc$ntRef, ignore.case=T) +refC <- grepl("C", qc$ntRef, ignore.case=T) +refG <- grepl("G", qc$ntRef, ignore.case=T) +refT <- grepl("T", qc$ntRef, ignore.case=T) +varA <- grepl("A", qc$ntVar, ignore.case=T) +varC <- grepl("C", qc$ntVar, ignore.case=T) +varG <- grepl("G", qc$ntVar, ignore.case=T) +varT <- grepl("T", qc$ntVar, ignore.case=T) +varN <- grepl(".", qc$ntVar, ignore.case=T) +callA <- grepl("^A", qc$ntVar, ignore.case=T) +callC <- grepl("^C", qc$ntVar, ignore.case=T) +callG <- grepl("^G", qc$ntVar, ignore.case=T) +callT <- grepl("^T", qc$ntVar, ignore.case=T) + +callList <- list(callA, callC, callG, callT) +varList <- list(varA, varC, varG, varT) +refList <- list(refA, refC, refG, refT) + +tots <- c( +rep(sum(qc$nRef[refA], qc$nVar[refA]), 4), +rep(sum(qc$nRef[refC], qc$nVar[refC]), 4), +rep(sum(qc$nRef[refG], qc$nVar[refG]), 4), +rep(sum(qc$nRef[refT], qc$nVar[refT]), 4)) + +nvar <- c( +rep(sum(qc$nVar[refA]), 4), +rep(sum(qc$nVar[refC]), 4), +rep(sum(qc$nVar[refG]), 4), +rep(sum(qc$nVar[refT]), 4)) + +nref <- c( +rep(sum(qc$nRef[refA]), 4), +rep(sum(qc$nRef[refC]), 4), +rep(sum(qc$nRef[refG]), 4), +rep(sum(qc$nRef[refT]), 4)) + +nts <- c("A", "C", "G", "T") +sumTrans <- data.frame(trans=paste(rep(nts, each=4), rep(nts, 4), sep=":"), cnt=rep(0, 16), tot=tots, nvar=nvar, nref=nref) + +for (i in 1:4) { + pos <- (i - 1) * 4 +for (j in 1:4) { +# print(sum(refList[[i]] & varList[[j]])) + + cnt <- sum(qc[refList[[i]] & varList[[j]], 8 + j]) + if (i == j) { +# cnt <- sum(qc[refList[[i]] & varN, 8 + j]) + cnt <- NA + } + sumTrans$cnt[pos + j] <- cnt + #print(cnt) +}} +#totalNT <- sum(qc$nVar) + sum(qc$nRef) +sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor +#sumTrans$cnt / totalNT -> sumTrans$cor +#sumTrans$cnt / min(sumTrans$cnt, na.rm=T) -> sumTrans$cor +#print(sumTrans) + +pCor <- rep(1, nrow(qc)) +for (i in 1:4) { + pos <- (i - 1) * 4 +for (j in 1:4) { + if (i != j) { + pCor[refList[[i]] & callList[[j]]] <- sumTrans$cor[pos + j] + } + +}} +return(pCor) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/lib/perl/perAmpliconAnalysis.pl Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,366 @@ +#!/usr/bin/perl -w + +use strict; + +my $bam = shift; +my $ref = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/ref/hg19/bwa-5/hg19.fa"; +my $manifest = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; +my $base = shift || "output"; +my $samtools = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/bin/samtools/samtools-0.1.18/samtools"; +my $fai = $ref . ".fai"; +my $Qthreshold = 10; +my $QavgLim = 20; + +open FAI, "<$fai"; +my %idx = (); +print STDOUT "Reading fa index ... "; +while (<FAI>) { + chomp; + my @row = split(/\t/, $_); + $idx{$row[0]} = [@row]; +} +print STDOUT "done\n"; + +close FAI; +open REF, "<$ref"; + +my %stats = (); +my %manif = (); +my %targets = (); +my %probe = (); +my %hash = (); + +open M, "<$manifest"; +while (<M>) { last if (/\[Probes\]/) } +readline(M); +while (<M>) { + chomp; + if (/\[Targets\]/) { + my $h = readline M; + chomp $h; + my @H = split(/\t/, $h); + last; + } + my @row = split(/\t/, $_); + $probe{$row[2]}{probe} = [@row]; + $probe{$row[2]}{ULSO} = $row[9]; + $probe{$row[2]}{DLSO} = $row[11]; +} + +while (<M>) { + chomp; + s/\s+$//; + my @row = split(/\t/, $_); + push @{$targets{$row[3]}{$_}}, $row[0] foreach ($row[4] .. $row[5]); + # $manif{$aTarget} = [@row]; + my $aTarget = $row[0] . "-" . $row[3] . ":". "$row[4]-$row[5]"; + if (not exists($stats{$aTarget}{target})) { + $stats{$aTarget}{target} = [@row]; + $stats{$aTarget}{ln} = $row[5] - $row[4] + 1; + $stats{$aTarget}{n} = 0; + $stats{$aTarget}{sam} = []; + $stats{$aTarget}{depth} = 0; + $stats{$aTarget}{covs} = []; + $stats{$aTarget}{chr} = $row[3]; + $stats{$aTarget}{start} = $row[4]; + $stats{$aTarget}{end} = $row[5]; + $stats{$aTarget}{ULSO} = $probe{$row[0]}{ULSO}; + $stats{$aTarget}{DLSO} = $probe{$row[0]}{DLSO}; + $stats{$aTarget}{assayStart} = $row[4] + length($probe{$row[0]}{ULSO}); + $stats{$aTarget}{assayEnd} = $row[5] - length($probe{$row[0]}{DLSO}); + } +# print $row[0] . "\n"; + foreach my $i (0 .. 5) { + foreach my $j (0 .. 5) { +# print $row[4] + $i .":". ($row[5] - $row[4] + $j) .":". $row[0] . "\n"; +# print $row[4] + $i .":". ($row[5] - $row[4] - $j) .":". $row[0] . "\n"; +# print $row[4] - $i .":". ($row[5] - $row[4] + $j) .":". $row[0] . "\n"; +# print $row[4] - $i .":". ($row[5] - $row[4] - $j) .":". $row[0] . "\n"; + $hash{$row[3]}{$row[4] + $i}{$row[5] - $row[4] + $j} = $aTarget; + $hash{$row[3]}{$row[4] + $i}{$row[5] - $row[4] - $j} = $aTarget; + $hash{$row[3]}{$row[4] - $i}{$row[5] - $row[4] + $j} = $aTarget; + $hash{$row[3]}{$row[4] - $i}{$row[5] - $row[4] - $j} = $aTarget; + } + } +# sleep 1; +} +close M; + +# samtools view -b 25MUT5.bam chr9:133738302-133738491 | samtools calmd - /gsdata/tmp/TSACP/ampliconPipeLine/ref/hg19/bwa-5/hg19.fa | head + +#foreach my $amp (keys(%stats)) { + +# print $amp . "\n"; +# my @SAM = (); + # Fetch reads +# my $coord = $stats{$amp}{chr} .":".$stats{$amp}{start}."-".$stats{$amp}{end}; +# my $ln = $stats{$amp}{ln}; +# print $coord . " $ln\n"; + +# Open output +open QC, ">$base.qc.ann.txt"; +open QC2, ">$base.qc2.ann.txt"; +open TARGET, ">$base.qc.targets.txt"; + +#TODO Remove stampy check +my $stampy = 0; +open SAMH, "$samtools view -H $bam |"; +while (<SAMH>) { + $stampy = 1 if (/PN:stampy/); + print STDERR "STAMPY SPOTTED!!!" if (/PN:stampy/); +} +close SAMH; + +open SAM, "$samtools view $bam |"; +#open SAM, "$samtools view -b $bam | $samtools calmd - $ref |"; +# open SAM, "$samtools view -b $bam $coord | $samtools calmd - $ref |"; +while (<SAM>) { + last unless (/^@/); +} +my $cnt = 0; +my %hsh = (); +my $pamp = "."; + +#Print header + +print QC "#" . join("\t", qw/chr pos amp dp ntRef ntVar nRef nVar nA nC nG nT nN ins del/) . "\n"; +print QC2 "#" . join("\t", qw/read chr pos amp event/) . "\n"; +print TARGET "#" . join("\t", qw/amp chr start end assayStart assayEnd depth/) . "\n"; +while (<SAM>) { + # Skip stampy reads? Nope, stampy is no longer needed + #TODO Remove stampy check +# next if ($stampy == 1 && ! /XP:Z:BWA/); + chomp; + my @row = split(/\t/, $_); + my $l = 0; + my $cig = $row[5]; + $cig =~ s/(\d+)[MD]/$l+=$1/eg; + + my $amp = $hash{$row[2]}{$row[3]}{$l} || next; + #print "$row[2] $row[3] $l $amp\n"; + + push @{$stats{$amp}{sam}}, [@row]; + $stats{$amp}{depth}++; + if (($pamp ne ".") && ($amp ne $pamp)) { + print STDOUT "Flushing $pamp $stats{$pamp}{depth}\n"; +# print TARGET join("\t", $pamp, map { $stats{$pamp}{$_} } qw/chr start end assayStart assayEnd depth/) . "\n"; + my $data = &call($stats{$pamp}{sam}); + &flush($data, $stats{$pamp}{chr}, $pamp, $stats{$pamp}{assayStart}, $stats{$pamp}{assayEnd}); + $stats{$pamp}{sam} = []; + } + $pamp = $amp; + $cnt++; +} + +close QC; +close QC2; +foreach my $pamp (keys %stats) { + print TARGET join("\t", $pamp, map { $stats{$pamp}{$_} || "NA"} qw/chr start end assayStart assayEnd depth/) . "\n"; +} +close TARGET; + + +# print join("\n", map {$hsh{$_} . ":" . $_} keys(%hsh)) . "\n"; +# print $cnt . "\n"; sleep 1; + close SAM; +# $stats{$amp}{depth} = $cnt; +# my $data = &call(\@SAM); +# &flush($data, $stats{$amp}{chr}, $amp); + +#} + +#foreach my $amp (keys(%stats)) { + +# print $amp . ":" . scalar(@{$stats{$amp}{sam}}) . "\n"; +#} + +sub call { + my $SAM = shift; + + my $ppos = 0; + my $pchr = ""; + my %data = (); + my $refSeq = ""; + my $c = 0; + my $col_chr = 2; + my $col_read = 9; + my $col_qual = 10; + my $col_pos = 3; + my $col_cigar = 5; + my $refSeqPad = "P"; + my %cooc = (); + my $cnt = 1; + foreach my $r (0 .. $#$SAM) { + my @row = @{$SAM->[$r]}; + my $read = $row[$col_read]; + my $qual = $row[$col_qual]; + my $pos = $row[$col_pos]; + my @cig = (); + my $aln = 0; + + # Calculate mean read quality and skip if it's below threshold + my $QSum = 0; + my $Qlen = length($qual); + + $QSum += ord($qual) foreach 1 .. $Qlen; + + my $Qavg = $QSum / $Qlen - 33; + next if ($Qavg < $QavgLim); + + while ($row[$col_cigar] =~ /(\d+)(\D)/g) { + push @cig, [$1, $2]; + $aln += $1; + } + if ($ppos != $pos) { + my $offset = $idx{$row[$col_chr]}->[2]; + my $nl = int (($row[$col_pos] - 1) / $idx{$row[$col_chr]}->[3]); + $offset += $row[$col_pos] + $nl - 1; + seek REF, $offset, 0; + $refSeqPad = substr($refSeq, -1, 1); + read REF, $refSeq, 1000;# length($read) * 5; + $refSeq =~ s/\s//g; + $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. $aln); + $ppos = $pos; + } + + foreach my $cigE (@cig) { + my $n = $cigE->[0]; + if ($cigE->[1] eq "I") { + my $rpos = $pos - $row[$col_pos]; + my $insert = substr($refSeq, $rpos - 1, 1) or print STDERR "Outside?" . $rpos . ":" . length($refSeq) . " $pos\n"; + $insert .= substr($read, 0, $n, ""); + my $qinsert .= substr($qual, 0, $n, ""); + push @{$data{$row[$col_chr]}{$pos - 1}{"IR"}{$insert}}, $r; + $data{$row[$col_chr]}{$pos - 1}{"I"}{$insert}++; +# push @{$cooc{$pos - 1 }{$insert}}, $cnt; + # $cooc{($pos - 1) .":".$insert}{$cnt} = 0; + } + elsif ($cigE->[1] eq "M") { + my $mseq = substr($read, 0, $n, ""); + my $mqual = substr($qual, 0, $n, ""); + foreach my $nt (0 .. (length($mseq) - 1)) { + $data{$row[$col_chr]}{$pos + $nt}{"DP"}++; + my $ntq = substr($mqual, $nt, 1); + my $ntn = substr($mseq, $nt, 1); + # if (ord($ntq) - 33 < $Qthreshold) { + # $ntn = "N"; + # } + $data{$row[$col_chr]}{$pos + $nt}{"NT"}{$ntn}++; + push @{$data{$row[$col_chr]}{$pos + $nt}{"NTR"}{$ntn}}, $r if (uc($ntn) ne uc($data{$row[$col_chr]}{$pos + $nt}{refNT})); +# if (($ntn ne $data{$row[$col_chr]}{$pos + $nt}{"refNT"}) && ($ntn ne "N")) { + #push @{$cooc{$pos + $nt}{$ntn}}, $cnt; + # $cooc{($pos + $nt) .":".$ntn}{$cnt} = 0; +# } + } + $pos += $n; + + } + elsif ($cigE->[1] eq "D") { + my $rpos = $pos - $row[$col_pos]; + my $deletion = substr($refSeq, $rpos - 1, $n + 1); # Substring out of string error ? + push @{$data{$row[$col_chr]}{$pos - 1}{"DR"}{$deletion}}, $r; + $data{$row[$col_chr]}{$pos - 1}{"D"}{$deletion}++; + #push @{$cooc{$pos - 1 }{$deletion}}, $cnt; + # $cooc{($pos - 1) . ":" . $deletion}{$cnt} = 0; + $pos += $n; + } + } + $cnt++; + } + #my $thresh = scalar(@$SAM) * .05; + #&coocCalc(\%cooc, \%data, $thresh); + return \%data; +} + +sub coocCalc { + my $cooc = shift; + my $data = shift; + my $thresh = shift; + my %rev = (); + # Filter low frequency variants + foreach my $k (keys(%$cooc)) { + if (scalar(keys(%{$cooc->{$k}})) < $thresh) { + delete($cooc->{$k}); + next; + } + print STDERR "$k : $thresh : " . join(":", sort {$a cmp $b} keys(%{$cooc->{$k}})) . "\n"; + } + my @muts = keys(%{$cooc}); + foreach my $i (0 .. $#muts) { +# my %hsh = map { $_ => 0 } keys(%{$cooc{$muts[$i]}}); + foreach my $j (($i + 1) .. $#muts) { + my $score = 0; + foreach my $m (keys(%{$cooc->{$muts[$i]}})) { + if (exists($cooc->{$muts[$j]}{$m})) { + $score++; + } + } + print STDERR $muts[$i] .":". $muts[$j] . ":" . $score . "\n"; sleep 1; + } + } + + #{read}{mutation} + #{mutation}{read} + sleep 1; +} + +sub flush { + my $data = shift; + my $chr = shift; + my $amp = shift; + my $s = shift; + my $e = shift; + return unless (exists($data->{$chr})); + print STDOUT "printing ... "; + my %reads = (); # read->pos->nt +# foreach my $p (sort {$a <=> $b} keys(%{$data->{$chr}})) { +# unless (($p >= $s) && ($p <= $e)) { +# next; +# } + foreach my $p ($s .. $e) { + my $posdat = $data->{$chr}{$p} || next; + next unless (exists($posdat->{DP})); + my $refNT = uc($posdat->{refNT}); + my @varOrd = sort { $posdat->{NT}{$b} <=> $posdat->{NT}{$a} } grep {$_ ne "N"} grep { $_ ne $refNT } keys(%{$posdat->{NT}}); + my $seqNT = join("/", @varOrd); + #my $refCNT = scalar(@{$posdat->{NT}{$refNT} || []}); + my $refCNT = $posdat->{NT}{$refNT} || 0; + my $varCNT = 0; + #$varCNT += scalar(@{$posdat->{NT}{$_}}) foreach (@varOrd); + #$varCNT += $posdat->{NT}{$_} foreach (@varOrd); + $varCNT = ($varOrd[0])?$posdat->{NT}{$varOrd[0]}:0; + my $Istr = "."; + my $Dstr = "."; + if ($varOrd[0]) { + $reads{$_}{$p} = "$refNT/$varOrd[0]" foreach (@{$posdat->{NTR}{$varOrd[0]}}); + } + if (exists($posdat->{I})) { + $Istr = join("|", map { $_ . ":" . $posdat->{I}{$_} } keys(%{$posdat->{I}})); + foreach my $I (keys(%{$posdat->{IR}})) { + $reads{$_}{$p} = "$refNT/$I" foreach (@{$posdat->{IR}{$I}}); + } + } + if (exists($posdat->{D})) { + $Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})); + foreach my $D (keys(%{$posdat->{DR}})) { + $reads{$_}{$p} = "$D/$refNT" foreach (@{$posdat->{DR}{$D}}); + } + } + #$Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})) if exists($posdat->{D}); + print QC join("\t", $chr, $p, $amp, + $posdat->{DP} || 0, + $posdat->{refNT} || ".", + $seqNT || ".", + $refCNT, $varCNT, + #(map { scalar(@{$posdat->{NT}{$_} || []})} qw(A C G T N)), $Istr, $Dstr, + (map { $posdat->{NT}{$_} || 0 } qw(A C G T N)), $Istr, $Dstr, + ) . "\n"; + # delete $data->{$chr}{$p}; + } + delete $data->{$chr}; + foreach my $r (sort { $a <=> $b } keys(%reads)) { + print QC2 join("\t", $r, $chr, $_, $amp, $reads{$r}{$_}) . "\n" foreach (sort {$a <=> $b} keys(%{$reads{$r}})); + } + print STDOUT "done\n"; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/lib/perl/qc2vcf.pl Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,135 @@ +#!/usr/bin/perl + +use strict; + +my $qc = shift; + +my $minDp = 100; +my $minVarDp = 5; +my $minVaf = 0.01; + +my $base = (split(/\//, $qc))[-1]; +my $header = qq(##fileformat=VCFv4.1 +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth"> +##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele Distribution"> +##FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele Ballance nref/nref+nvar"> +##INFO=<ID=TARGET,Number=1,Type=String,Description="TSACP Target name"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $base +); + +my $chr = 0; +my $pos = 1; +my $target = 2; +my $dp = 3; +my $ref = 4; +my $var = 5; +my $nref = 6; +my $nvar = 7; +my $nA = 8; +my $nC = 9; +my $nG = 10; +my $nT = 11; +my $nN = 12; +my $ins = 13; +my $del = 14; +my $pval = 15; +my $pvala = 16; +my $varQual = 17; +my $insQual = 18; +my $delQual = 19; + +my %acgt = (A => 0, C => 1, G => 2, T => 3); +print $header; +open QC, "<$qc"; +while (<QC>) { + chomp; + next if (/^#/); + next if (/^X\./); + my @row = split(/\t/, $_); + next if ($row[$target] eq "."); + + my $VAR = substr($row[$var], 0, 1); + my $REF = $row[$ref]; + my $nvarall = $row[$nvar]; + my $indel = $row[$ins] . $row[$del]; + if ($row[$nvar] > 0 || $indel eq "..") { + my %ord = ( A => $row[$nA], C => $row[$nC], G => $row[$nG], T => $row[$nT], N => $row[$nN] ); + $ord{uc($REF)} = -1; # Exclude ref from sort + $ord{N} = -1; # Exclude N! + my @order = sort { $ord{$b} <=> $ord{$a} } keys(%ord); + my $dpVar = $ord{$order[0]}; + my $VAR = $order[0]; + my $skip = 0; + my $tot = $row[$nref] + $dpVar; + my $vaf = ($tot > 0)?$dpVar / $tot:"NA"; # Excluding other alleles... + #$skip++ if ($tot == 0); + #$skip++ if ($ord{$order[0]} == $ord{$order[1]}); # Multiallelic, skipping for now + #$skip++ if ($dpVar == 0); # Skip if dpVar is zero, can occur when N is the only variant. Above line also protects for this. + #$skip++ if ($dpVar < $minVarDp); + #$skip++ if ($row[$dp] < $minDp); + #$skip++ if ($vaf < $minVaf); + my $gt = "$row[$ref]/$VAR"; + my $qual = $row[$varQual] || 0; + $skip++ if ($qual == 0); + my $filter = 0; + my $info = "TARGET=$row[$target]"; + my $format = "DP:AD:AB"; + my $sample = "$row[$dp]:$row[$nref],$dpVar:$vaf"; + print join("\t", @row[$chr, $pos], ".", $REF, $VAR, $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); + } + # INDEL + if ($row[$ins] ne ".") { + my $skip = 0; + # Modify coordinte to conform to VCF? + my %inss = split(/[\|\:]/, $row[$ins]); + my @keys = sort { $inss{$b} <=> $inss{$a} } keys %inss; +# if ($inss{$keys[0]} > $row[$nvar]) { +# $nvarall = $inss{$keys[0]}; +# $VAR = $keys[0]; +# $row[$dp] += $nvarall; +# } + my $nins = $inss{$keys[0]}; + my $DP = $row[$dp]; + my $nREF = $DP - $nins; + #$skip++ if ($nins < $minVarDp); + #$skip++ if ($DP < $minDp); + my $vaf = $nins / $row[$dp]; + #$skip++ if ($vaf < $minVaf); + my $gt = "$row[$ref]/$keys[0]"; + my $qual = $row[$insQual]; + $skip++ if ($qual == 0); + my $filter = 0; + my $info = "TARGET=$row[$target]"; + my $format = "DP:AD:AB"; + my $sample = "$DP:$nREF,$nins:$vaf"; + print join("\t", @row[$chr, $pos], ".", $REF, $keys[0], $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); + } + if ($row[$del] ne ".") { + my $skip = 0; + # Modify coordinte to conform to VCF? + my %dels = split(/[\|\:]/, $row[$del]); + my @keys = sort { $dels{$b} <=> $dels{$a} } keys %dels; +# if ($dels{$keys[0]} > $row[$nvar]) { +# $nvarall = $dels{$keys[0]}; +# $REF = $keys[0]; +# $row[$dp] += $nvarall; +# } + my $ndel = $dels{$keys[0]}; + my $DP = $row[$dp]; + my $nREF = $DP - $ndel; + #$skip++ if ($ndel < $minVarDp); + #$skip++ if ($DP < $minDp); + my $vaf = $ndel / $DP; + #$skip++ if ($vaf < $minVaf); + my $gt = "$keys[0]/$row[$ref]"; + my $qual = $row[$delQual]; + $skip++ if ($qual == 0); + my $filter = 0; + my $info = "TARGET=$row[$target]"; + my $format = "DP:AD:AB"; + my $sample = "$DP:$nREF,$ndel:$vaf"; + print join("\t", @row[$chr, $pos], ".", $keys[0], $row[$ref], $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); + } +} +close QC; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/lib/perl/qcFilt.pl Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,54 @@ +#!/usr/bin/perl + +use strict; + +my $qcQual = shift; +my $output = shift; + +my $minDp = shift || 100; +my $minVar = shift || 10; +my $minIns = shift || $minVar; +my $minDel = shift || $minVar; +my $minVarQ = shift || 100; +my $minInsQ = shift || 200; +my $minDelQ = shift || 200; + +open QC, "<$qcQual"; +my $head = readline QC; +chomp; +$head =~ s/\s+$//; +my @rhead = split(/\t/, $head); +my $coln = 0; +my %col = map { $_ => $coln++ } @rhead; +open OUT, ">$output.qc.ann.qual.filt.txt"; +print OUT "$head\n"; + +while (<QC>) { + my $line = $_; + my @row = split(/\t/, $_); + my $key = $row[$col{"X.chr"}] . ":" . $row[$col{pos}]; + next if ($row[$col{dp}] < $minDp); + # Var + if ($row[$col{qScore}] >= $minVarQ && $row[$col{nVar}] > $minVar) { + print OUT $line; + next; + } + # Ins + if ($row[$col{qScoreI}] >= $minInsQ) { + $row[$col{ins}] =~ /:(\d+)/; + if ($1 >= $minIns) { + print OUT $line; + next; + } + } + # Del + if ($row[$col{qScoreD}] >= $minDelQ) { + $row[$col{del}] =~ /:(\d+)/; + if ($1 >= $minDel) { + print OUT $line; + next; + } + } +} + +close OUT;
--- a/falco/misc/addQc.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -#!/usr/bin/perl - -use strict; - -my $file = shift; -my $qc = shift; -my %crds = (); -open F, "<$file"; -my $fhead = readline F; -chomp $fhead; -print $fhead . "\t" . join("\t", qw/dp dpref dpvar vaf/) . "\n"; -while (<F>) { - chomp; - my @row = split(/\t/, $_, -1); -# print STDERR scalar(@row) . "\n"; - push @{$crds{$row[0]}{$row[1]}}, [@row]; -} -close F; - -# INDELS? -my %ntcol = (A => 8, C => 9, G => 10, T => 11); -open QC, "<$qc"; -while (<QC>) { - chomp; - my @row = split(/\t/, $_); - next if ($row[2] eq "."); - my $muts = $crds{$row[0]}{$row[1]} || undef; - next unless $muts; - foreach my $mut (@$muts) { - my $rl = length($mut->[3]); - my $vl = length($mut->[4]); - - my $refDP = $row[$ntcol{uc($row[4])}]; - - if ($rl > $vl && $row[14] ne ".") { # Deletion - my %dels = split(/[\|\:]/, $row[14]); - my @del = sort { $dels{$b} <=> $dels{$a} } keys(%dels); - my $deldp = $dels{$del[0]}; - print join("\t", @{$mut}, $row[3], $row[6] - $deldp, $deldp, $deldp / $row[3]) . "\n"; - - } - elsif ($rl < $vl && $row[13] ne ".") { # Insertion - my %inss = split(/[\|:]/, $row[13]); - my @ins = sort { $inss{$b} <=> $inss{$a} } keys(%inss); - my $insdp = $inss{$ins[0]}; - print join("\t", @{$mut}, $row[3], $row[6] - $insdp, $insdp, $insdp / $row[3]) . "\n"; - } - elsif ($rl == $vl) { - my @varnts = sort { $row[$ntcol{$b}] <=> $row[$ntcol{$a}] } split(/\//, $row[5]); - next if ($row[$ntcol{$varnts[0]}] == $row[$ntcol{$varnts[1]}]); # Equeal variant counts - my $vardp = $row[$ntcol{$varnts[0]}]; - print join("\t", @{$mut}, $row[3], $row[6], $vardp, $vardp / ($row[6] + $vardp)) . "\n"; - } - - } - next; -# if (exists($crds{$row[0]}{$row[1]}) && length($crds{$row[0]}{$row[1]}->[3]) > 1) { # In case of snp - if (exists($crds{$row[0]}{$row[1]})) { # && length($crds{$row[0]}{$row[1]}->[3]) > 1) { # In case of snp - print join("\t", @{$_}, $row[3], $row[6], $row[7], $row[7] / $row[3]) . "\n" foreach @{$crds{$row[0]}{$row[1]}}; - } - if ($row[14] ne "." && exists($crds{$row[0]}{$row[1]})) { # In case of deletion! - my %dels = split(/[\|\:]/, $row[14]); - my @del = sort { $dels{$b} <=> $dels{$a} } keys(%dels); - $row[7] = $dels{$del[0]}; - print join("\t", @{$_}, $row[3], $row[6] - $row[7], $row[7], $row[7] / $row[3]) . "\n" foreach @{$crds{$row[0]}{$row[1]}}; - } - if ($row[13] ne "." && exists($crds{$row[0]}{$row[1]})) { # In case of insertion - my %inss = split(/[\|:]/, $row[13]); - my @ins = sort { $inss{$b} <=> $inss{$a} } keys(%inss); - $row[7] = $inss{$ins[0]}; - print join("\t", @{$_}, $row[3], $row[6] - $row[7], $row[7], $row[7] / $row[3]) . "\n" foreach @{$crds{$row[0]}{$row[1]}}; - } -} -close QC;
--- a/falco/misc/addQual.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -#!/usr/bin/Rscript -args <- commandArgs(T) -qcFile <- args[1] -output <- args[2] -funcR <- args[3] -lociFiltFile <- args[4] - -read.delim(lociFiltFile, header=F) -> lociFiltD -lociFilt <- paste(paste("chr", lociFiltD[,1], sep=""), lociFiltD[,2], sep=":") - -source(funcR) -read.delim(qcFile, header=T) -> qc - -#addQual(qc) -> qc.qual -addQualTransCor(qc, lociFilt) -> qc.qual -#addQualVarCor(qc) -> qc.qual - -write.table(qc.qual, output, row.names=F, col.names=T, quote=F, sep="\t") -#write.table(qc[selection,], output, row.names=F, col.names=T, quote=F, sep="\t") - -
--- a/falco/misc/alignmentStats.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my $targetBed = shift; -my @bams = @ARGV; -$|= 1; - -foreach my $bam (@bams) { - my $file = `basename $bam`; - chomp $file; - my $res0 = `samtools idxstats $bam`; - my @Qdat = (); - my %Q = (); - my $mapped = 0; - my $ontarget = 0; - my $unmapped = 0; - while ($res0 =~ /(\S+)\s(\S+)\s(\S+)\s(\S+)\n/g) { - if ($1 ne "*") { - $mapped += $3; - $unmapped += $4; - } - else { - $unmapped += $3; - $unmapped += $4; - } - } - my %Qcon = map { chr($_ + 33) => $_ } (0 .. 40); - open PIPE, "samtools view -XF0x014 -L $targetBed $bam | cut -f11 |"; - while (<PIPE>) { - my @is = (0 .. (length($_) - 2)); - $ontarget++; - foreach my $i (@is) { - $Qdat[$i][$Qcon{substr($_, $i, 1)}]++; - } - } - - open PIPE, "samtools view -XF0x004 -f0x010 -L $targetBed $bam | cut -f11 |"; - while (<PIPE>) { - my @is = reverse(0 .. (length($_) - 2)); - $ontarget++; - foreach my $i (@is) { - $Qdat[$i][$Qcon{substr($_, $i, 1)}]++; - } - } - - open QUAL, ">$file.qual.tsv"; - print QUAL join("\t", "pos", 0 .. $#Qdat) . "\n"; - my $q0 = 0; - my $q10 = 0; - my $q20 = 0; - my $q30 = 0; - my $qtot = 0; - foreach my $p (0 .. $#Qdat) { - print QUAL join("\t", $p, map { $Qdat[$p][$_] || 0 } (0 .. $#{$Qdat[$p]})) . "\n"; - foreach my $q (0 .. $#{$Qdat[$p]}) { - $qtot += $Qdat[$p][$q] || 0; - $q30 += $Qdat[$p][$q] || 0 if ($q >= 30); - $q20 += $Qdat[$p][$q] || 0 if ($q >= 20 && $q < 30); - $q10 += $Qdat[$p][$q] || 0 if ($q >= 10 && $q < 20); - $q0 += $Qdat[$p][$q] || 0 if ($q < 10); - } - } - close QUAL; - - my $offtarget = $mapped - $ontarget; - print join("\t", $file, $mapped, $ontarget, $offtarget, $unmapped, $q30/$qtot, $q20/$qtot, $q10/$qtot, $q0/$qtot) . "\n"; - -}
--- a/falco/misc/attachGff.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -#!/usr/bin/perl -w -# -# TODO: tiled targets give wrong length... -use strict; - -my $gff = shift; -my $covtable = shift; - -my $QCrep = shift || "qc.txt"; - -my %targets = (); -my %stats = (); -my %manif = (); -open M, "<$gff"; -while (<M>) { - if (/^track/) { - my $h = readline M; - chomp $h; - my @H = split(/\t/, $h); -# print $_ . ":" . $H[$_] . "\n" foreach (0 .. $#H); - last; - } -} -while (<M>) { - chomp; - s/\s+$//; - my @row = split(/\t/, $_); - push @{$targets{$row[0]}{$_}}, $row[8] foreach ($row[3] .. $row[4]); - $manif{$row[8]} = [@row]; - if (not exists($stats{$row[8]}{dat})) { - $stats{$row[8]}{dat} = [@row]; - $stats{$row[8]}{ln} = $row[4] - $row[3] + 1; - $stats{$row[8]}{n} = 0; - $stats{$row[8]}{covs} = []; - } -} -close M; - -open C, "<$covtable"; -while (<C>) { - chomp; - my @row = split(/\t/, $_); - $#row = 13; - if (exists($targets{$row[0]}{$row[1]})) { - foreach my $t (@{$targets{$row[0]}{$row[1]}}) { - $stats{$t}{n}++; - $stats{$t}{covSum} += $row[2]; - push @{$stats{$t}{covs}}, $row[2]; - } - } - print join("\t", @row[0 .. 1], - (join("|", @{$targets{$row[0]}{$row[1]} || ["."]} )), - (@row[2 .. 11]), - (map { $_ || "." } @row[12 .. $#row]), - ). "\n"; -# sleep 1; -} -close C; - -# Calc assay stats -open QC, ">$QCrep"; -foreach my $t (sort keys %stats) { - my @covs = sort {$a <=> $b} @{$stats{$t}{covs}}; - my $mean = ($stats{$t}{n} != 0)?$stats{$t}{covSum} / $stats{$t}{n}:0; - #print join("\t", @{$stats{$t}{dat}}, $mean, map { $stats{$t}{$_} } qw/ln n/). "\n"; - print QC join("\t", $t, sprintf("%.2f", $mean), map { $stats{$t}{$_} } qw/ln n/). "\n"; - -} -close QC;
--- a/falco/misc/attachManifest.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -#!/usr/bin/perl -w -# -# TODO: tiled targets give wrong length... -use strict; - -my $manifest = shift; -my $covtable = shift; - -my $QCrep = shift || "qc.txt"; - -my %targets = (); -my %stats = (); -my %manif = (); -open M, "<$manifest"; -while (<M>) { last if (/\[Probes\]/) } -readline(M); -while (<M>) { - chomp; - if (/\[Targets\]/) { - my $h = readline M; - chomp $h; - my @H = split(/\t/, $h); -# print $_ . ":" . $H[$_] . "\n" foreach (0 .. $#H); - last; - } - my @row = split(/\t/, $_); - $stats{$row[2]}{probe} = [@row]; - $stats{$row[2]}{ULSO} = $row[9]; - $stats{$row[2]}{DLSO} = $row[11]; - - -} -while (<M>) { - chomp; - s/\s+$//; - my @row = split(/\t/, $_); - push @{$targets{$row[3]}{$_}}, $row[0] foreach ($row[4] .. $row[5]); - $manif{$row[0]} = [@row]; - if (not exists($stats{$row[0]}{target})) { - $stats{$row[0]}{target} = [@row]; - $stats{$row[0]}{ln} = $row[5] - $row[4] + 1; - $stats{$row[0]}{n} = 0; - $stats{$row[0]}{covs} = []; - $stats{$row[0]}{chr} = $row[3]; - $stats{$row[0]}{start} = $row[4]; - $stats{$row[0]}{end} = $row[5]; - $stats{$row[0]}{assayStart} = $row[4] + length($stats{$row[0]}{ULSO}); - $stats{$row[0]}{assayEnd} = $row[5] - length($stats{$row[0]}{DLSO}); - } -} -close M; - -open C, "<$covtable"; -while (<C>) { - chomp; - my @row = split(/\t/, $_); - $#row = 13; - if (exists($targets{$row[0]}{$row[1]})) { - foreach my $t (@{$targets{$row[0]}{$row[1]}}) { - $stats{$t}{n}++; - $stats{$t}{covSum} += $row[2]; - push @{$stats{$t}{covs}}, $row[2]; - } - } - print join("\t", @row[0 .. 1], - (join("|", @{$targets{$row[0]}{$row[1]} || ["."]} )), - (@row[2 .. 11]), - (map { $_ || "." } @row[12 .. $#row]), - ). "\n"; -# sleep 1; -} -close C; - -# Calc assay stats -open QC, ">$QCrep"; -foreach my $t (sort keys %stats) { - my @covs = sort {$a <=> $b} @{$stats{$t}{covs} || []}; - my $mean = ($stats{$t}{n} != 0)?$stats{$t}{covSum} / $stats{$t}{n}:0; - #print join("\t", @{$stats{$t}{dat}}, $mean, map { $stats{$t}{$_} } qw/ln n/). "\n"; - print QC join("\t", $t, sprintf("%.2f", $mean), map { $stats{$t}{$_} } qw/ln n chr start end assayStart assayEnd/). "\n"; - -} -close QC;
--- a/falco/misc/checkRunComplete.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -#!/usr/bin/perl - -use strict; - -# Check RTAcomplete.txt -# Check existence in AnalisysOutput - -my $base = "/ccagc/lib/pipelines/TSACP/falco/misc"; -my $getData = "$base/getData.pl"; -my $startAn = "$base/startAnalysis.pl"; - -my $Project = shift or die "No project specified!\n"; -my $AnalysisOutput = shift || "./"; #"/ccagc/data/SeqAnalysis/$Project"; - -my $MiSeqOutput = shift || "/ccagc/data/processing/MiSeqOutput/"; - - -my $LOG = shift || "$AnalysisOutput/log/$Project.log"; - -if (! -d "$AnalysisOutput/log") { - mkdir "$AnalysisOutput/log"; -} - -my %log = (); -open LOG, "<$LOG"; -while (<LOG>) { - chomp; - # runDir date - my @row = split(/\t/, $_); - $log{$row[0]} = [@row]; -} -close LOG; - -my @runs = `find $MiSeqOutput -maxdepth 2 -iname "RTAComplete.txt"`; -my %runHsh = (); - -foreach my $r (@runs) { - chomp; - my $runDir = `dirname $r`; - chomp $runDir; - if (exists($log{$runDir})) { - print STDERR "$runDir previously checked\n"; - next; - } - my @row = split(/\//, $runDir); - my @run = split(/\_/, $row[$#row]); - my $outDir = $AnalysisOutput . "/" . join("_", @run[0 .. 2]); - my $baseDir = $AnalysisOutput; - if (-e $outDir) { - print STDERR "$outDir exists, skipping\n"; - } else { - print STDERR "perl $getData $runDir $Project\n"; - system("perl $getData $runDir $Project $baseDir"); - print STDERR "perl $startAn $outDir\n"; - system("perl $startAn $outDir"); - open LOG, ">>$LOG"; - print LOG join("\t", $runDir, scalar(localtime())) . "\n"; - close LOG; - } -} -
--- a/falco/misc/errorRate.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -#!/usr/bin/perl -w -# - -use strict; -my @files = @ARGV; -foreach my $file (@files) { -my $ref = 0; -my $var = 0; - -my $file = shift; - -open F, "<$file"; -my $header = readline F; # Skip header -chomp $header; -my @hrow = split(/\t/, $header); -my $ci = 0; -my %col = (); -$col{$_} = $ci++ foreach (@hrow); - - -while (<F>) { - chomp; - my @row = split(/\t/, $_); - #next if ($row[2] eq "."); - #print join("\t", $row[6], $row[7]) . "\n"; sleep 1; - my $ntRef = uc($row[4]); - $ref += $row[$col{"n$ntRef"}]; - $var += $row[$col{"n$_"}] foreach (grep { $_ ne $ntRef } qw/A C G T/); -} - -close F; -my @path = split(/\//, $file); -my $rate = $var / ($ref + $var) * 100; -#print STDERR "$var/$ref -> $rate%\n"; -print "$path[$#path]\t$var\t$ref\t$rate\n"; -}
--- a/falco/misc/filter.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -#!/usr/bin/Rscript -args <- commandArgs(T) -resFile <- args[1] -qcFile <- args[2] -varLim <- args[3] -dpLim <- args[4] -quants <- args[5] -output <- args[6] - -read.delim(resFile, header=T) -> d -read.delim(qcFile, header=T) -> qc - -# Calculate errorrate per amplicon -amps <- unique(qc$X.amp) -for (i in amps) { - sel <- qc$X.amp == amps - prob <- sum(qc$nVar[sel]) / (sum(qc$nRef) + sum(qc$nVar)) - pees <- pbinom(qc$nVar[sel], qc$nRef + qc$nVar, prob, lower.tail=F) - Qscore <- -10 * log10(pees) - -} - -quantile(d$vaf, as.numeric(quants), na.rm=T) -> vafCut - -sel1 <- d$vaf > vafCut -sel2 <- d$dp > dpLim -sel3 <- d$dpvar > varLim - -sel <- sel1 & sel2 & sel3 -write.table(d[sel,], paste(output, "res.f1.tsv", sep="."), row.names=F, col.names=T, quote=F, sep="\t") - -dir.create(output) -setwd(output) - -png(paste(output, "vafcut", "png", sep=".")) -plot(density(log10(d$vaf), na.rm=T), main=paste("VAF cutoff", vafCut, sep=" ")) -abline(v=log10(vafCut), col=2) -dev.off()
--- a/falco/misc/filter.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#!/usr/bin/perl -w -# - -use strict; - -my $file = shift; -my $canonicals = shift; - -my %can = (); -my %nm = (); - -open CAN, "<$canonicals"; - -while (<CAN>) { - chomp; - my @row = split(/\t/, $_); - $can{$row[0]} = @row[1 .. $#row]; - my $pri = 0; - $nm{$_} = $pri++ foreach @row[1 .. $#row]; -# print STDERR join(":", @row[0,1]) . "\n"; sleep 1; -} - -open F, "<$file"; -my $head = readline(F); -chomp $head; -print $head . "\tvaf\n"; -my @rowHead = split(/\t/, $head); -my $colN = 0; -my %col = map { -# print STDERR $_ . " $colN\n"; - $_ => $colN++ } @rowHead; - -while (<F>) { - chomp; - my $line = $_; - my @row = split(/\t/, $_); - #g12 t15 - next unless (exists($can{$row[$col{Gene_Name}]})); - my $trans = $row[$col{Transcript_ID}]; - $trans =~ s/\..*$//; - - if (not exists($nm{$trans})) { - print STDERR "Unknown transcript: $row[$col{Gene_Name}] $trans\n"; - next; - } - elsif ($nm{$trans} != 0) { - print STDERR "Non cannonical: $row[$col{Gene_Name}] $trans\n"; - next; - } - - #next unless ($nm{$trans} == 0); - - # Do not filter out clinicvar loci - #print $_ . "\n" if ($row[$col{Tag}] eq "Clinvar"); - next if ($row[$col{Tag}] eq "Clinvar"); -# print STDERR $row[15]; sleep 1; -# print STDERR $nm{$row[15]}; sleep 1; - -#CODON_CHANGE_PLUS_CODON_DELETION -#CODON_DELETION -#DOWNSTREAM -#EXON -#FRAME_SHIFT -#INTRON -#NON_SYNONYMOUS_CODING -#SPLICE_SITE_ACCEPTOR -#SYNONYMOUS_CODING -#UPSTREAM -#UTR_3_PRIME - - # Filter INTERGENIC - next if ($row[$col{Context}] eq "INTERGENIC"); - - # Filter SYNONYMOUS_CODING - # Dubbel mutatie BRAF -# next if ($row[$col{Context}] eq "SYNONYMOUS_CODING"); - - # Filter INTRON - next if ($row[$col{Context}] eq "INTRON"); - - # Filter dbSNP -# next if ($row[2] ne "."); - - # Filter depth - next if ($row[$col{DP}] < 100); - - my ($nref, $nvar) = split(/,/, $row[$col{AD}]); - # Filter var depth -# print STDERR "DEBUG: " . $nvar . "\n"; sleep 1; - next if ($nvar < 10); - - my $vaf = $nvar / ($nref + $nvar); -# print STDERR "DEBUG: " . $vaf . "\n"; - # Filter vaf - next if ($vaf < 0.01); - - - print $_ . "\t$vaf\n"; -} -close F;
--- a/falco/misc/filterQC.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,118 +0,0 @@ -#!/usr/bin/Rscript -args <- commandArgs(T) -qcFile <- args[1] -varLim <- as.numeric(args[2]) -dpLim <- as.numeric(args[3]) -quants <- as.numeric(args[4]) -output <- args[5] - -read.delim(qcFile, header=T) -> d - -vaf <- d$nVar / (d$nRef + d$nVar) - -sapply(1:nrow(d), function(x) { - if (d$del[x] != ".") { - dels <- matrix(unlist(strsplit(as.character(d$del[x]), c("[:|]"))), byrow=T, ncol=2) - delRanks <- rank(dels[,2]) - delDp <- as.numeric(dels[rev(delRanks)[1],2]) - if (delDp > varLim) { - return(T) - } - } - if (d$ins[x] != ".") { - ins <- matrix(unlist(strsplit(as.character(d$ins[x]), c("[:|]"))), byrow=T, ncol=2) - insRanks <- rank(ins[,2]) - insDp <- as.numeric(ins[rev(insRanks)[1],2]) - if (insDp > varLim) { - return(T) - } - - } - return(F) -}) -> indelSel - - -#dels <- matrix(unlist(strsplit(d$del, ":|")) -#inss <- strsplit(d$ins, ":|") -#d$vafDel -#d$vafIns - -quantile(vaf, as.numeric(quants), na.rm=T) -> vafCut - -sel1 <- vaf > vafCut -sel2 <- d$dp > dpLim -sel3 <- (d$nVar > varLim) | indelSel - -sel <- sel1 & sel2 & sel3 -write.table(d[sel,], paste(output, "res.sigfilt.tsv", sep="."), row.names=F, col.names=F, quote=F, sep="\t") - -dir.create(output) -setwd(output) - -png(paste(output, "vafcut", "png", sep=".")) -plot(density(log10(vaf), na.rm=T), main=paste("VAF cutoff", vafCut, sep=" ")) -abline(v=log10(vafCut), col=2) -dev.off() - -ampls <- unique(d$amp) - -pdf(paste(output, "pdf", sep="."), width=14) -sapply(ampls, function(x) { - sel <- d[,3] == x - main = x -# plot(density(as.numeric(as.vector(d[sel,8]))), main=main) -# hist(as.numeric(as.vector(d[sel,8])), breaks=range(d[sel,8])[2], main=main) - - # Get indels - dels <- (d[,15] != ".") & sel - ins <- (d[,14] != ".") & sel - - pNoise <- sum(d$nVar[sel]) / (sum(d$nRef[sel]) + sum(d$nVar[sel])) - print(pNoise) - pVals <- ppois(d$nVar[sel], (d$nVar[sel] + d$nRef[sel]) * pNoise, lower.tail=F) - Qval <- -10*log10(pVals) - noiseThrs <- qpois(0.01, (d$nVar[sel] + d$nRef[sel]) * pNoise) - - plot(d[sel,2], d[sel,4], pch=20, type="s", ylim=c(0, max(d[sel,4])), main=main) - lines(d[sel,2], d[sel,7], pch=20, type="s", col=2) - lines(d[sel,2], d[sel,8], pch=20, type="s",col=3) - - ampMax <- max(d[sel,4]) - - for (idx in which(dels)) { - matrix(unlist(strsplit(as.character(as.vector(d[idx,15])), "[:|]")), ncol=2, byrow=T) -> delDat - nchar(delDat[,1]) -> lngts - dpths <- as.numeric(delDat[,2]) - rect(d[idx,2] + 1, ampMax - dpths , d[idx,2] + lngts, ampMax, col="#00000040") - } - - for (idx in which(ins)) { - matrix(unlist(strsplit(as.character(as.vector(d[idx,14])), "[:|]")), ncol=2, byrow=T) -> insDat - nchar(insDat[,1]) -> lngts - dpths <- as.numeric(insDat[,2]) - for (i in 1:ncol(insDat)) { - polygon( - c(d[idx,2], d[idx,2] - (.5 * lngts[i]), d[idx, 2] + (.5 * lngts[i])), - c(ampMax, ampMax - dpths[i], ampMax - dpths[i]), - , col="#00000040") - } - } - - #abline(v=d[dels,2], col=4) - #abline(v=d[ins,2], col=5) - - vaf <- d[sel,8]/(d[sel,7] + d[sel,8]) - - plot(density(vaf), main=main) - - hist(vaf, breaks=100, main=main) - - plot(d[sel,2], d[sel,8]/(d[sel,7] + d[sel,8]), pch=20, cex=.5, ylim=c(0,1), main=main) - points(d[sel,2], noiseThrs / (d[sel,7] + d[sel,8]), col=2, pch=20) - plot(d[sel,2], log10(d[sel,8]/(d[sel,7] + d[sel,8])), pch=20, cex=.5, ylim=c(-4,0), main=main) - points(d[sel,2], log10(noiseThrs / (d[sel,7] + d[sel,8])), col=2, pch=20) - print(x) -# print(sum(sel)) - }) - -dev.off()
--- a/falco/misc/func.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,569 +0,0 @@ -#!/usr/bin/Rscript -#args <- commandArgs(T) -#qcFile <- args[1] -#output <- args[2] - -#read.delim(qcFile, header=T) -> qc - -addQual <- function(qc) { - -qc$del <- as.character(as.vector(qc$del)) -qc$ins <- as.vector(qc$ins) -qc$pVal <- 1 -qc$pValAdj <- 1 -#qc$pValPois <- 1 -qc$qScore <- 0 -qc$qScoreI <- 0 -qc$qScoreD <- 0 - -pVal.I <- rep(1, nrow(qc)) -pVal.D <- rep(1, nrow(qc)) - -delSel <- qc$del != "." -data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[delSel]), "\\|")), ":")), ncol=2, byrow=T)) -> dels -dels$ln <- nchar(as.vector(dels$X1)) -colnames(dels) <- c("seq", "occ", "ln") -delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) - -insSel <- qc$ins != "." -data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[insSel]), "\\|")), ":")), ncol=2, byrow=T)) -> inss -inss$ln <- nchar(as.vector(inss$X1)) -colnames(inss) <- c("seq", "occ", "ln") -insPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) - -# Calculate errorrate per amplicon -amps <- unique(qc$amp) -for (i in amps) { - print(i) - sel <- qc$amp == i - prob <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) - #prob <- median(qc$nVar[sel] / (qc$nRef[sel] + qc$nVar[sel])) - pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob, lower.tail=F) - qc$pVal[sel] <- pees -# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) -# qc$pValPois[sel] <- pois - - # Seperate for indel/deletion events - selDels <- delSel & sel - if (sum(selDels) > 0) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 - dels2$ln <- nchar(as.vector(dels2$X1)) - colnames(dels2) <- c("seq", "occ", "ln") - dels2$occ <- as.numeric(as.vector(dels2$occ)) - } - for (j in which(selDels)) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels - dels$ln <- nchar(as.vector(dels$X1)) - colnames(dels) <- c("seq", "occ", "ln") - dels$occ <- as.numeric(as.vector(dels$occ)) - #dels$pDel <- delPees[as.integer(dels$ln)] - #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) - dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) - dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) - dels$Q <- -10 * log10(dels$pVal) - - high <- order(dels$occ, -dels$Q, decreasing=T)[1] - qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") - qc$qScoreD[j] <- dels$Q[high] - pVal.D[j] <- dels$pVal[high] - } - selIns <- insSel & sel - if (sum(selIns) > 0) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 - inss2$ln <- nchar(as.vector(inss2$X1)) - colnames(inss2) <- c("seq", "occ", "ln") - inss2$occ <- as.numeric(as.vector(inss2$occ)) - } - for (j in which(selIns)) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss - inss$ln <- nchar(as.vector(inss$X1)) - colnames(inss) <- c("seq", "occ", "ln") - inss$occ <- as.numeric(as.vector(inss$occ)) - #inss$pIns <- insPees[as.integer(inss$ln)] - #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) - inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) - inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) - inss$Q <- -10 * log10(inss$pVal) - - high <- order(inss$occ, -inss$Q, decreasing=T)[1] - qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") - qc$qScoreI[j] <- inss$Q[high] - pVal.I[j] <- inss$pVal[high] - } - print(sum(-10 * log10(pees) > 100)) - print(sum(qc$qScoreI[selIns] > 100)) - print(sum(qc$qScoreD[selDels] > 100)) -} - -p.adjust(qc$pVal) -> qc$pValAdj --10 * log(p.adjust(pVal.I)) -> qc$qScoreI --10 * log(p.adjust(pVal.D)) -> qc$qScoreD -qc$qScore <- -10 * log10(qc$pValAdj) -#qc$qScore[qc$pValAdj == 0] <- 1000 -qc$qScore[qc$qScore > 1000] <- 1000 -qc$qScoreI[qc$qScoreI > 1000] <- 1000 -qc$qScoreD[qc$qScoreD > 1000] <- 1000 -qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) -dpfilt <- as.numeric(qc$dp) >= 100 -#varfilt <- as.numeric(qc$nVar) >= 10 - -selection <- qsel & dpfilt - -print(paste("Filtered out: ", sum(!selection), sep="")) -print(paste("Variants selected: ", sum(selection), sep="")) -return(qc) -} - -addQualTransCor <- function(qc, lociFilt) { - - -# lociFilt contains snp, cosmic and clinvar positions - -qc$del <- as.character(as.vector(qc$del)) -#qc$del <- as.character(as.vector(qc$del)) -qc$ins <- as.character(as.vector(qc$ins)) -qc$pVal <- 1 -qc$pValAdj <- 1 -#qc$pValPois <- 1 -qc$qScore <- 0 -qc$qScoreI <- 0 -qc$qScoreD <- 0 - -pVal.I <- rep(1, nrow(qc)) -pVal.D <- rep(1, nrow(qc)) - -rle(as.vector(qc$ntRef)) -> srle -hompols <- srle$lengths >= 5 -homPosS <- cumsum(srle$lengths)[hompols] -homPosE <- cumsum(srle$lengths)[which(hompols) - 1] -homFilt <- rep(F, nrow(qc)) -homFilt[homPosS] <- T -homFilt[homPosE] <- T - -delSel <- qc$del != "." & !homFilt -if (sum(delSel > 0)) { - - -data.frame(matrix(unlist(strsplit(unlist(strsplit(qc$del[delSel], "\\|")), ":")), ncol=2, byrow=T)) -> dels -dels$ln <- nchar(as.vector(dels$X1)) -colnames(dels) <- c("seq", "occ", "ln") -delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) -} - -insSel <- qc$ins != "." & !homFilt -if (sum(insSel) > 0) { -data.frame(matrix(unlist(strsplit(unlist(strsplit(qc$ins[insSel], "\\|")), ":")), ncol=2, byrow=T)) -> inss -inss$ln <- nchar(as.vector(inss$X1)) -colnames(inss) <- c("seq", "occ", "ln") -insPees <- ppois(1:50, mean(rep(inss$ln, inss$occ)), lower.tail=F) -} -# Calculate transition bias - - -#calcTransCor(qc) -> pCor -globalProb <- sum(qc$nVar) / (sum(qc$nRef) + sum(qc$nVar)) -# Calculate errorrate per amplicon -amps <- unique(qc$amp) -for (i in amps) { - print(i) - sel <- qc$amp == i - prob1 <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) - prob <- prob1 * calcTransCor(qc[sel,], lociFilt) - pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob , lower.tail=F) - qc$pVal[sel] <- pees -# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) -# qc$pValPois[sel] <- pois - - # Seperate for indel/deletion events - selDels <- delSel & sel - if (sum(selDels) > 0) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 - dels2$ln <- nchar(as.vector(dels2$X1)) - colnames(dels2) <- c("seq", "occ", "ln") - dels2$occ <- as.numeric(as.vector(dels2$occ)) - - for (j in which(selDels)) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels - dels$ln <- nchar(as.vector(dels$X1)) - colnames(dels) <- c("seq", "occ", "ln") - dels$occ <- as.numeric(as.vector(dels$occ)) - #dels$pDel <- delPees[as.integer(dels$ln)] - #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) - dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) - dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) - dels$Q <- -10 * log10(dels$pVal) - - high <- order(dels$occ, -dels$Q, decreasing=T)[1] - qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") - qc$qScoreD[j] <- dels$Q[high] - pVal.D[j] <- dels$pVal[high] - } - } - selIns <- insSel & sel - if (sum(selIns) > 0) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 - inss2$ln <- nchar(as.vector(inss2$X1)) - colnames(inss2) <- c("seq", "occ", "ln") - inss2$occ <- as.numeric(as.vector(inss2$occ)) - - for (j in which(selIns)) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss - inss$ln <- nchar(as.vector(inss$X1)) - colnames(inss) <- c("seq", "occ", "ln") - inss$occ <- as.numeric(as.vector(inss$occ)) - #inss$pIns <- insPees[as.integer(inss$ln)] - #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) - inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) - inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) - inss$Q <- -10 * log10(inss$pVal) - - high <- order(inss$occ, -inss$Q, decreasing=T)[1] - qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") - qc$qScoreI[j] <- inss$Q[high] - pVal.I[j] <- inss$pVal[high] -} } - print(sum(-10 * log10(pees) > 100)) - print(sum(qc$qScoreI[selIns] > 100)) - print(sum(qc$qScoreD[selDels] > 100)) -} - -p.adjust(qc$pVal) -> qc$pValAdj --10 * log(p.adjust(pVal.I)) -> qc$qScoreI --10 * log(p.adjust(pVal.D)) -> qc$qScoreD -qc$qScore <- -10 * log10(qc$pValAdj) -#qc$qScore[qc$pValAdj == 0] <- 1000 -qc$qScore[qc$qScore > 1000] <- 1000 -qc$qScoreI[qc$qScoreI > 1000] <- 1000 -qc$qScoreD[qc$qScoreD > 1000] <- 1000 -qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) -dpfilt <- as.numeric(qc$dp) >= 100 -#varfilt <- as.numeric(qc$nVar) >= 10 - -selection <- qsel & dpfilt - -print(paste("Filtered out: ", sum(!selection), sep="")) -print(paste("Variants selected: ", sum(selection), sep="")) -return(qc) -} - - -addQualVarCor <- function(qc) { -# Corrected for variant occurence - -qc$del <- as.character(as.vector(qc$del)) -qc$ins <- as.vector(qc$ins) -qc$pVal <- 1 -qc$pValAdj <- 1 -#qc$pValPois <- 1 -qc$qScore <- 0 -qc$qScoreI <- 0 -qc$qScoreD <- 0 - -pVal.I <- rep(1, nrow(qc)) -pVal.D <- rep(1, nrow(qc)) - -delSel <- qc$del != "." -data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[delSel]), "\\|")), ":")), ncol=2, byrow=T)) -> dels -dels$ln <- nchar(as.vector(dels$X1)) -colnames(dels) <- c("seq", "occ", "ln") -delPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) - -insSel <- qc$ins != "." -data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[insSel]), "\\|")), ":")), ncol=2, byrow=T)) -> inss -inss$ln <- nchar(as.vector(inss$X1)) -colnames(inss) <- c("seq", "occ", "ln") -insPees <- ppois(1:50, mean(rep(dels$ln, dels$occ)), lower.tail=F) - -# Calculate base bias per run -sum(qc$nA[grepl("A", qc$ntRef, ignore.case=T)]) -> refA -sum(qc$nA[!grepl("A", qc$ntRef, ignore.case=T)]) -> varA -sum(qc$nC[grepl("C", qc$ntRef, ignore.case=T)]) -> refC -sum(qc$nC[!grepl("C", qc$ntRef, ignore.case=T)]) ->varC -sum(qc$nG[grepl("G", qc$ntRef, ignore.case=T)]) -> refG -sum(qc$nG[!grepl("G", qc$ntRef, ignore.case=T)]) -> varG -sum(qc$nT[grepl("T", qc$ntRef, ignore.case=T)]) -> refT -sum(qc$nT[!grepl("T", qc$ntRef, ignore.case=T)]) -> varT - -varA / (refA + varA) -> errA -varC / (refC + varC) -> errC -varG / (refG + varG) -> errG -varT / (refT + varT) -> errT -c(errA, errC, errG, errT) / mean(c(errA, errC, errG, errT)) -> errACGT - -errMat <- qc[,9:12] -errMat[grepl("A", qc$ntRef, ignore.case=T),1] <- 0 -errMat[grepl("C", qc$ntRef, ignore.case=T),2] <- 0 -errMat[grepl("G", qc$ntRef, ignore.case=T),3] <- 0 -errMat[grepl("T", qc$ntRef, ignore.case=T),4] <- 0 - -pCor <- rep(1, nrow(qc)) -pCor[grepl("^A", qc$ntVar, ignore.case=T)] <- errACGT[1] -pCor[grepl("^C", qc$ntVar, ignore.case=T)] <- errACGT[2] -pCor[grepl("^G", qc$ntVar, ignore.case=T)] <- errACGT[3] -pCor[grepl("^T", qc$ntVar, ignore.case=T)] <- errACGT[4] - -# Calculate errorrate per amplicon -amps <- unique(qc$amp) -for (i in amps) { - print(i) - sel <- qc$amp == i - prob <- sum(qc$nVar[sel]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) - #prob <- median(qc$nVar[sel] / (qc$nRef[sel] + qc$nVar[sel])) - pees <- pbinom(qc$nVar[sel], qc$nRef[sel] + qc$nVar[sel], prob * pCor[sel], lower.tail=F) - qc$pVal[sel] <- pees -# pois <- ppois(qc$nVar[sel], (qc$nRef + qc$nVar) * prob, lower.tail=F) -# qc$pValPois[sel] <- pois - - # Seperate for indel/deletion events - selDels <- delSel & sel - if (sum(selDels) > 0) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[selDels]), "\\|")), ":")), ncol=2, byrow=T)) -> dels2 - dels2$ln <- nchar(as.vector(dels2$X1)) - colnames(dels2) <- c("seq", "occ", "ln") - dels2$occ <- as.numeric(as.vector(dels2$occ)) - } - for (j in which(selDels)) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$del[j]), "\\|")), ":")), ncol=2, byrow=T)) -> dels - dels$ln <- nchar(as.vector(dels$X1)) - colnames(dels) <- c("seq", "occ", "ln") - dels$occ <- as.numeric(as.vector(dels$occ)) - #dels$pDel <- delPees[as.integer(dels$ln)] - #dels$pVal <- ppois(as.numeric(dels$occ), dels$pDel, lower.tail=F) - dels$pDel <- sapply(dels$ln, function(x) {sum(dels2$occ[dels2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) - dels$pVal <- pbinom(dels$occ, qc$dp[j], dels$pDel, lower.tail=F) - dels$Q <- -10 * log10(dels$pVal) - - high <- order(dels$occ, -dels$Q, decreasing=T)[1] - qc$del[j] <- paste(dels$seq[high], dels$occ[high], sep=":") - qc$qScoreD[j] <- dels$Q[high] - pVal.D[j] <- dels$pVal[high] - } - selIns <- insSel & sel - if (sum(selIns) > 0) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[selIns]), "\\|")), ":")), ncol=2, byrow=T)) -> inss2 - inss2$ln <- nchar(as.vector(inss2$X1)) - colnames(inss2) <- c("seq", "occ", "ln") - inss2$occ <- as.numeric(as.vector(inss2$occ)) - } - for (j in which(selIns)) { - data.frame(matrix(unlist(strsplit(unlist(strsplit(as.vector(qc$ins[j]), "\\|")), ":")), ncol=2, byrow=T)) -> inss - inss$ln <- nchar(as.vector(inss$X1)) - colnames(inss) <- c("seq", "occ", "ln") - inss$occ <- as.numeric(as.vector(inss$occ)) - #inss$pIns <- insPees[as.integer(inss$ln)] - #inss$pVal <- ppois(as.numeric(inss$occ), inss$pIns, lower.tail=F) - inss$pIns <- sapply(inss$ln, function(x) {sum(inss2$occ[inss2$ln == x]) / (sum(qc$nRef[sel]) + sum(qc$nVar[sel])) }) - inss$pVal <- pbinom(inss$occ, qc$dp[j], inss$pIns, lower.tail=F) - inss$Q <- -10 * log10(inss$pVal) - - high <- order(inss$occ, -inss$Q, decreasing=T)[1] - qc$ins[j] <- paste(inss$seq[high], inss$occ[high], sep=":") - qc$qScoreI[j] <- inss$Q[high] - pVal.I[j] <- inss$pVal[high] - } - print(sum(-10 * log10(pees) > 100)) - print(sum(qc$qScoreI[selIns] > 100)) - print(sum(qc$qScoreD[selDels] > 100)) -} - -p.adjust(qc$pVal) -> qc$pValAdj --10 * log(p.adjust(pVal.I)) -> qc$qScoreI --10 * log(p.adjust(pVal.D)) -> qc$qScoreD -qc$qScore <- -10 * log10(qc$pValAdj) -#qc$qScore[qc$pValAdj == 0] <- 1000 -qc$qScore[qc$qScore > 1000] <- 1000 -qc$qScoreI[qc$qScoreI > 1000] <- 1000 -qc$qScoreD[qc$qScoreD > 1000] <- 1000 -qsel <- (qc$qScore >= 100 & qc$nVar >= 10) | (qc$qScoreI >= 200) | (qc$qScoreD >= 200) -dpfilt <- as.numeric(qc$dp) >= 100 -#varfilt <- as.numeric(qc$nVar) >= 10 - -selection <- qsel & dpfilt - -print(paste("Filtered out: ", sum(!selection), sep="")) -print(paste("Variants selected: ", sum(selection), sep="")) -return(qc) -} - -#addQual(qc) -> qc -#write.table(qc, output, row.names=F, col.names=T, quote=F, sep="\t") -#write.table(qc[selection,], output, row.names=F, col.names=T, quote=F, sep="\t") - -calcTrans <- function(qcRaw, lociFilt = NULL) { - -sel <- rep(T, nrow(qcRaw)) -if (!is.null(lociFilt)) { -paste(qcRaw$X.chr, qcRaw$pos, sep=":") -> qcpos -sel <- ! qcpos %in% lociFilt -} -qc <- qcRaw[sel,] - -print(sum(sel)) - -# Calculate transition bias -refA <- grepl("A", qc$ntRef, ignore.case=T) -refC <- grepl("C", qc$ntRef, ignore.case=T) -refG <- grepl("G", qc$ntRef, ignore.case=T) -refT <- grepl("T", qc$ntRef, ignore.case=T) -varA <- grepl("A", qc$ntVar, ignore.case=T) -varC <- grepl("C", qc$ntVar, ignore.case=T) -varG <- grepl("G", qc$ntVar, ignore.case=T) -varT <- grepl("T", qc$ntVar, ignore.case=T) -varN <- grepl(".", qc$ntVar, ignore.case=T) -callA <- grepl("^A", qc$ntVar, ignore.case=T) -callC <- grepl("^C", qc$ntVar, ignore.case=T) -callG <- grepl("^G", qc$ntVar, ignore.case=T) -callT <- grepl("^T", qc$ntVar, ignore.case=T) - -callList <- list(callA, callC, callG, callT) -varList <- list(varA, varC, varG, varT) -refList <- list(refA, refC, refG, refT) - -#tots <- c( -#rep(sum(qc$nRef[refA], qc$nVar[refA]), 4), -#rep(sum(qc$nRef[refC], qc$nVar[refC]), 4), -#rep(sum(qc$nRef[refG], qc$nVar[refG]), 4), -#rep(sum(qc$nRef[refT], qc$nVar[refT]), 4)) - -nvar <- c( -rep(sum(qc$nC[refA], qc$nG[refA], qc$nT[refA]), 4), -rep(sum(qc$nA[refC], qc$nG[refC], qc$nT[refC]), 4), -rep(sum(qc$nA[refG], qc$nC[refG], qc$nT[refG]), 4), -rep(sum(qc$nA[refT], qc$nC[refT], qc$nG[refT]), 4)) - -ncall <- c( -rep(sum(qc$nVar[refA]), 4), -rep(sum(qc$nVar[refC]), 4), -rep(sum(qc$nVar[refG]), 4), -rep(sum(qc$nVar[refT]), 4)) - -nref <- c( -rep(sum(qc$nRef[refA]), 4), -rep(sum(qc$nRef[refC]), 4), -rep(sum(qc$nRef[refG]), 4), -rep(sum(qc$nRef[refT]), 4)) - -tots <- nref + nvar - -nts <- c("A", "C", "G", "T") -sumTrans <- data.frame(trans=paste(rep(nts, each=4), rep(nts, 4), sep=":"), cnt=rep(0, 16), tot=tots, nvar=nvar, nref=nref, ncall=ncall) - -for (i in 1:4) { - pos <- (i - 1) * 4 -for (j in 1:4) { -# print(sum(refList[[i]] & varList[[j]])) - - cnt <- sum(qc[refList[[i]] & varList[[j]], 8 + j]) - if (i == j) { -# cnt <- sum(qc[refList[[i]] & varN, 8 + j]) - cnt <- NA - } - sumTrans$cnt[pos + j] <- cnt - print(cnt) -}} - -#sumTrans$cnt / sumTrans$nvar / sumTrans$tot * 1000000 -> tmp -sumTrans$cnt / sumTrans$tot * 1000000 -> tmp - -#totalNT <- sum(qc$nVar) + sum(qc$nRef) -#sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor -sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor -tmp / median(tmp, na.rm=T) -> sumTrans$cor2 -#sumTrans$cnt / totalNT -> sumTrans$cor -#sumTrans$cnt / min(sumTrans$cnt, na.rm=T) -> sumTrans$cor - - -return(sumTrans) - -} - -calcTransCor <- function(qcRaw, lociFilt = NULL) { - -calcTrans(qcRaw, lociFilt) -> sumTrans - -pCor <- rep(1, nrow(qcRaw)) -paste(qcRaw$ntRef, substr(qcRaw$ntVar, 1, 1), sep=":") -> qcTrans - -for (i in c("A", "C", "G", "T")) { -for (j in c("A", "C", "G", "T")) { - if (i != j) { - tTrans <- paste(i, j, sep=":") - pCor[grepl(tTrans, qcTrans, ignore.case=T)] <- sumTrans$cor2[sumTrans$trans == tTrans] - } - -}} -return(pCor) -} - - -calcTransCorOld <- function(qc) { -# Calculate transition bias -refA <- grepl("A", qc$ntRef, ignore.case=T) -refC <- grepl("C", qc$ntRef, ignore.case=T) -refG <- grepl("G", qc$ntRef, ignore.case=T) -refT <- grepl("T", qc$ntRef, ignore.case=T) -varA <- grepl("A", qc$ntVar, ignore.case=T) -varC <- grepl("C", qc$ntVar, ignore.case=T) -varG <- grepl("G", qc$ntVar, ignore.case=T) -varT <- grepl("T", qc$ntVar, ignore.case=T) -varN <- grepl(".", qc$ntVar, ignore.case=T) -callA <- grepl("^A", qc$ntVar, ignore.case=T) -callC <- grepl("^C", qc$ntVar, ignore.case=T) -callG <- grepl("^G", qc$ntVar, ignore.case=T) -callT <- grepl("^T", qc$ntVar, ignore.case=T) - -callList <- list(callA, callC, callG, callT) -varList <- list(varA, varC, varG, varT) -refList <- list(refA, refC, refG, refT) - -tots <- c( -rep(sum(qc$nRef[refA], qc$nVar[refA]), 4), -rep(sum(qc$nRef[refC], qc$nVar[refC]), 4), -rep(sum(qc$nRef[refG], qc$nVar[refG]), 4), -rep(sum(qc$nRef[refT], qc$nVar[refT]), 4)) - -nvar <- c( -rep(sum(qc$nVar[refA]), 4), -rep(sum(qc$nVar[refC]), 4), -rep(sum(qc$nVar[refG]), 4), -rep(sum(qc$nVar[refT]), 4)) - -nref <- c( -rep(sum(qc$nRef[refA]), 4), -rep(sum(qc$nRef[refC]), 4), -rep(sum(qc$nRef[refG]), 4), -rep(sum(qc$nRef[refT]), 4)) - -nts <- c("A", "C", "G", "T") -sumTrans <- data.frame(trans=paste(rep(nts, each=4), rep(nts, 4), sep=":"), cnt=rep(0, 16), tot=tots, nvar=nvar, nref=nref) - -for (i in 1:4) { - pos <- (i - 1) * 4 -for (j in 1:4) { -# print(sum(refList[[i]] & varList[[j]])) - - cnt <- sum(qc[refList[[i]] & varList[[j]], 8 + j]) - if (i == j) { -# cnt <- sum(qc[refList[[i]] & varN, 8 + j]) - cnt <- NA - } - sumTrans$cnt[pos + j] <- cnt - print(cnt) -}} -#totalNT <- sum(qc$nVar) + sum(qc$nRef) -sumTrans$cnt / median(sumTrans$cnt, na.rm=T) -> sumTrans$cor -#sumTrans$cnt / totalNT -> sumTrans$cor -#sumTrans$cnt / min(sumTrans$cnt, na.rm=T) -> sumTrans$cor -print(sumTrans) - -pCor <- rep(1, nrow(qc)) -for (i in 1:4) { - pos <- (i - 1) * 4 -for (j in 1:4) { - if (i != j) { - pCor[refList[[i]] & callList[[j]]] <- sumTrans$cor[pos + j] - } - -}} -return(pCor) -}
--- a/falco/misc/getData.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -#!/usr/bin/perl - -use strict; - -# Read in path(s) and run bcl2fastq to fetch data into appropriate directories - -my $runDir = shift; -my $project = shift || die "Project required"; -my $baseDir = shift || "/ccagc/data/SeqAnalysis/$project"; -my $dry = 0; -my $outDir = undef; -(my $FCID = $runDir) =~ s/.*_(.*?)\/?$/$1/; - -if (not defined($outDir)) { - ($outDir = $runDir) =~ s/.*\/(.*_.*_.*)_.*/$1/; - $outDir = $baseDir ."/". $outDir; -} - -print STDERR localtime() . " : PATH: " . $runDir . "\n"; -print STDERR localtime() . " : BASEDIR: " . $baseDir . "\n"; -print STDERR localtime() . " : OUTDIR: " . $outDir . "\n"; -print STDERR localtime() . " : FCID: " . $FCID . "\n"; - -# open samplesheet -# Check run type and convert for bcl2fastq -my $col = 0; - -my @headOut = qw/FCID Lane SampleID SampleRef Index Description Control Recipe Operator SampleProject/; -my $Lane = 1; -my $SampleRef = "human"; -my $Control = "N"; -my $SampleProject = $project; -my %header = (); -open SAMPLE, "<$runDir/SampleSheet.csv" or die; -while (<SAMPLE>) { - chomp; - s/\s+$//; - my @row = split(/,/, $_); -# if (/^(.*),(.*)$/) { -# $header{$1} = $2; -# } - $header{$row[0]} = $row[1]; - last if (/\[Data\]/); -} - -if ($header{Assay} !~ /Amplicon/) { - print STDERR localtime() . " : Wrong assay, exiting.\n"; - exit; -} - -# Skipping project name check for now -#if ($header{"Project Name"} !~ /$project/) { -# print STDERR localtime() . " : Wrong project, exiting.\n"; -# exit; -#} - -my $Operator = $header{"Investigator Name"}; -my $Recipe = $header{"Workflow"}; - -my $head = readline(SAMPLE); -chomp $head; -my %headIn = map { $_ => $col++ } split(/,/, $head);#"Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description,Manifest,GenomeFolder"); - -my @samples = (); -my @ctrls = (); -while (<SAMPLE>) { - chomp; - my @row = split(/,/, $_); - print STDERR localtime() . " : " . join(":", @row) . "\n"; - my $bc = substr($row[$headIn{index}],0,7) ."-". substr($row[$headIn{index2}],0,7); - if ($row[$headIn{Sample_Project}] != /$SampleProject/) { - push @samples, join(",", $FCID, $Lane, $row[$headIn{Sample_ID}], $SampleRef, $bc, $row[$headIn{Description}], $Control, $Recipe, $Operator, $SampleProject) . "\n"; - } - elsif ($row[$headIn{Sample_Project}] != /CONTROL/i) { - push @ctrls, join(",", $FCID, $Lane, $row[$headIn{Sample_ID}], $SampleRef, $bc, $row[$headIn{Description}], $Control, $Recipe, $Operator, $SampleProject) . "\n"; - } - -} -close SAMPLE; - -if ($dry == 1) { - print STDERR localtime() . " : mkdir $outDir\n"; - print STDERR localtime() . " : " . join(",", @headOut) . "\n"; - print STDERR localtime() . " : " . join("", @samples); -} -elsif (-e $outDir) { - print STDERR localtime() . " : Folder $outDir exists, exiting\n"; - exit; -} -elsif ($#samples >= 0) { - print STDERR localtime() . " : mkdir $outDir\n"; - system("mkdir -p $outDir"); - open SAMPLEOUT, ">$outDir/SampleSheet.csv"; - print SAMPLEOUT join(",", @headOut) . "\n"; - print STDERR localtime() . " : " . join(",", @headOut) . "\n"; - print SAMPLEOUT join("", @samples, @ctrls); - print STDERR localtime() . " : " . join("", @samples, @ctrls); - close SAMPLEOUT; -} -else { - # Nothing to do exit! - print STDERR localtime() . " : Nothing to do for $SampleProject, exiting!"; - exit; -} - - -# run configureBCL2fastq -my $bcl2fqbin = "/usr/local/bin/configureBclToFastq.pl"; -my $bcl2fq = "$bcl2fqbin --no-eamss --input-dir $runDir/Data/Intensities/BaseCalls --output-dir $outDir/Unaligned --sample-sheet $outDir/SampleSheet.csv --mismatches 0 --fastq-cluster-count 0"; -my $make = "cd $outDir/Unaligned && nohup make && touch bcl2fq.done && cd .."; - -print STDERR localtime() . " : $bcl2fq\n"; -print STDERR localtime() . " : $make\n"; -if ($dry == 1) { - exit; -} - -my $pid1 = open BCL2FQ, "$bcl2fq 2>&1 |"; -while (<BCL2FQ>) { - print STDERR localtime() . " - $_"; -} -close BCL2FQ; - -my $pid2 = open MAKE, "$make 2>&1 |"; -while (<MAKE>) { - print STDERR localtime() . " - $_"; -} -close MAKE; - - -#my $rc1 = 0; #system($bcl2fq); -# run make -#if ($rc1 == 0) { -# my $rc2 = system($make); -#} -#else { -# print STDERR localtime() . " : Error or warning encountered :$rc1\n"; -# print STDERR localtime() . " : Run make manually\n"; -# print STDERR localtime() . " : $make\n"; -#}
--- a/falco/misc/mkHtmlReport.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,201 +0,0 @@ -#!/usr/bin/perl -w - -use strict; -use Spreadsheet::WriteExcel; - -$| = 1; -my $dir = shift; -my $outdir = shift || "./"; -my $pat = shift || ""; - -# QC -# Results -my @samples = (); -open INDEX, ">$outdir/index.html"; -my $htmlHead = qq( -<!DOCTYPE html> -<html> -<head> -<style type="text/css"> -body {font-family:arial;} -table {font-family:arial;border-collapse: collapse; font-size: smaller;} -th {border: 1px solid gray; padding: 5px;} -td {border: 1px solid gray; padding: 5px; text-align: right;} -</style> -</head> -<body> -); -print INDEX $htmlHead; -opendir DIR, "$dir"; -while (my $cd = readdir DIR) { - if ($cd =~ /(.*$pat)\.qc\.targets\.txt$/) { - my $sam = $1; -# next if ($sam =~ /R[12]/); - print STDERR $1 . "\n"; - push @samples, $1; - } -} -close DIR; - -print INDEX "<table>"; -print INDEX "<tr><th>Sample</th><th>BAM</th><th>snp</th><th>indel</th><th>readCnt</th><th>Amp > 100</th>\n"; -#foreach my $sam (sort @samples) { -# print INDEX "<tr><td><a href=$sam.html>$sam</a></td><td><a href=$sam.bam>BAM</a></td><td><a href=$sam.bam.bai>BAI</a></td></tr>\n"; - -#} -my %link = (); - -foreach my $sample (sort @samples) { - print STDERR "Processing $sample\n"; -# next if ($sample =~ /R[12]/); - - my $readCnt = 0; - my $amp100 = 0; - - open OUT, ">$outdir/$sample.html"; - open OUT2, ">$outdir/$sample.tsv"; - my $excelBook = Spreadsheet::WriteExcel->new("$outdir/$sample.xls"); - my $excel = $excelBook->add_worksheet(); - print OUT $htmlHead; - my %QC = (); - open QC, "<$dir/$sample.qc.targets.txt"; - readline QC; - print STDERR "Reading in $sample.qc.targets.txt\n"; - while (<QC>) { - chomp; - my @row = split(/\t/, $_); - my @id = split(/[\_\.\-:]/, $row[0]); - $readCnt += $row[-1]; # DP - $amp100++ if ($row[-1] >= 100); # - if ($#id != 10) { - $id[0] =~ /(\D+)(\d+)/; - $id[0] = $2; - unshift @id, $1; - } - $QC{$row[0]}{QC} = [@id, @row];# if ($id[0]); - foreach my $c ($row[4] .. $row[5]) { - $link{$id[-3] . ":" . $c}{$row[0]} = "Assay"; - } - foreach my $c ($row[2] .. $row[4], $row[5] .. $row[3]) { - $link{$id[-3] . ":" . $c}{$row[0]} = "LSO"; - } - } - close QC; - - open RES, "<$dir/$sample.res.filtered.tsv" or die "Unable to open $dir/$sample\n"; - my %uniq = (); - my $colCnt = 0; - my $resHead = readline(RES); - chomp $resHead; - $resHead =~ s/^#//; - $resHead =~ s/\s+$//; - my %resCol = map { $_ => $colCnt++ } split(/\t/, $resHead); - my @keyColsN = qw/QUAL Gene_Name Codon_Change Amino_Acid_change vaf DP AD Tag CHROM POS ID REF ALT Context Effect_Impact Functional_Class Amino_Acid_length Gene_Coding Transcript_ID Exon_Rank/; - #my @keyColsN = qw/QUAL Gene_Name Codon_Change Amino_Acid_change vaf DP AD Tag CHROM POS ID REF ALT Context Effect_Impact Functional_Class Amino_Acid_length Coding Transcript Exon/; -# my @keyColsN = qw/CHROM POS ID REF ALT QUAL DP AD vaf Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name Coding Transcript Exon Tag/; - my @keyColsI = map { $resCol{$_} } @keyColsN; -# print STDERR join(":", @keyColsN) . "\n"; -# print STDERR join(":", @keyColsI) . "\n"; -# sleep 10; - print STDERR "Processing results\n"; - while (<RES>) { - chomp; - my @row = split(/\t/, $_); - my $cpos = join(":", @row[0, 1]); - if (exists $link{$cpos}) { -# my $key = join(":", @row[0 .. 4,6, 9,10,11,12,14 .. 21]); - my $key = join(":", @row[@keyColsI]); - #print STDERR join(":", @keyColsI) . "\n"; -# print STDERR join(":", @row) . "\n"; sleep 1; - if (not exists($uniq{$key})) { - foreach my $locus (keys(%{$link{$cpos}})) { - next if ($link{$cpos}{$locus} eq "LSO"); - push @{$QC{$locus}{RES}}, [@row, $link{$cpos}{$locus}]; - # print STDERR "Adding $key to $locus\n\n"; #sleep 1; - } - $uniq{$key} = 0; - } - else { - # print STDERR $key . " : Exists\n\n"; #sleep 1; - } - } - } - close RES; - print OUT "<img src=\"$sample/$sample.vaf.png\">"; - print OUT "<img src=\"$sample/$sample.raf.png\">"; - print OUT "<img src=\"$sample/$sample.snv-q.png\">"; - print OUT "<img src=\"$sample/$sample.snv-q-zoom.png\">"; - print OUT "<img src=\"$sample/$sample.ins-q.png\">"; - print OUT "<img src=\"$sample/$sample.del-q.png\">"; - print OUT "<img src=\"$sample/$sample.amp-dp.png\">"; - print OUT "<img src=\"$sample/$sample.heat.png\">"; - print OUT "<img src=\"$sample/$sample.bias.png\">"; - print OUT "<img src=\"$sample/$sample.biasheat.png\">"; - #print OUT "<img src=\"$sample/$sample.vafcut.png\">"; - print OUT "<table border=1><tr><th>Download:</th><th><a href=\"$sample.tsv\">TSV</a></th>"; - print OUT "<th><a href=\"$sample.xls\">XLS</a></th></table>"; - print OUT "<table border=1>\n"; -# my @colnames = qw/depth chr pos id ref var qual DP AD vaf context impact effectClass codonChange AAChange RefSeqLength geneName RefSeqClass RefSeqID Exon Tag/; - my @colnames = ("depth", @keyColsN); - print OUT "<tr>" . join("", map { "<th>$_</th>" } ("Amplicon", "c","c2", "b", @colnames)) . "</tr>"; - print OUT2 join("\t", "Amplicon", @colnames) . "\n"; - my $excelAref = [["Amplicon", @colnames]]; - my %rescnt = (); - foreach my $locus (sort keys(%QC)) { - # my @targets = keys(%{$QC{$locus}{QC}}); -# print OUT "</td>"; - my $nres = 1; - $nres = scalar(@{$QC{$locus}{RES}}) if ($QC{$locus}{RES}); - - print OUT "<tr><td rowspan=\"$nres\">$locus</td>\n"; - print OUT "<td rowspan=\"$nres\"><a href=\"$sample/$sample.$locus.cov.png\">c</a></td>\n"; - print OUT "<td rowspan=\"$nres\"><a href=\"$sample/$sample.$locus.cov2.png\">c2</a></td>\n"; - print OUT "<td rowspan=\"$nres\"><a href=\"$sample/$sample.$locus.bias.png\">b</a></td>\n"; - print OUT "<td rowspan=\"$nres\">$QC{$locus}{QC}->[-1]</td>\n"; #<td rowspan=\"$nres\">"; - - foreach my $res (@{$QC{$locus}{RES}}) { - print OUT "<td>\n"; - print OUT join("</td><td>\n", @{$res}[@keyColsI]); - print OUT "</td></tr><tr>\n"; - print OUT2 join("\t", $locus, $QC{$locus}{QC}->[-1], @{$res}[@keyColsI]) . "\n"; - push @$excelAref, [$locus, $QC{$locus}{QC}->[-1], @{$res}[@keyColsI]]; - my $pl = $res->[$keyColsI[7]]; - my $ref = $res->[$keyColsI[11]]; - my $var = $res->[$keyColsI[12]]; -# print STDERR "$pl $ref $var\n"; sleep 1; - if (length($ref) == length($var)) { - $rescnt{$pl . "snp"}++; - } - else { - $rescnt{$pl . "indel"}++; - } -# $rescnt++; - } - print STDERR $locus . ":" . $nres . "\n"; - print STDERR $locus . ":" . join("-", @{$QC{$locus}{RES}}) . "\n"; - if (scalar(@{$QC{$locus}{RES}}) == 0) { #$nres == 0) { - print OUT2 join("\t", $locus, $QC{$locus}{QC}->[-1], ("-") x scalar(@keyColsI)) . "\n"; - push @$excelAref, [$locus, $QC{$locus}{QC}->[-1], ("-") x scalar(@keyColsI)]; - } - print OUT "</tr>\n"; - } - print OUT "</table>\n"; - print OUT "</body></html>\n"; - close OUT; - close OUT2; - $excel->write_col(0,0, $excelAref); - $excelBook->close(); - my @resCnt = map { $rescnt{$_} || 0 } qw/Customsnp Customindel/; - my $pctGood = sprintf("%.2f", $amp100 / scalar(keys(%QC)) * 100); - print INDEX "<tr><td><a href=$sample.html>$sample</a></td><td><a href=$sample.bam>BAM</a></td><td>$resCnt[0]</td><td>$resCnt[1]</td><td>$readCnt</td><td>$pctGood</td></tr>\n"; - -} - -print INDEX "</table>"; -print INDEX "<img src=\"alnStats.png\">"; -print INDEX "<img src=\"errStats.png\">"; -print INDEX "<img src=\"qualStats.png\">"; -print INDEX "</html>"; -close INDEX; - -
--- a/falco/misc/pairUp.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my $r1 = shift; -my $r2 = shift; -my $o1 = shift || "$r1.paired"; -my $o2 = shift || "$r2.paired"; -my $min = 10; -my %hsh = (); - -open R1, "<$r1"; -while (<R1>) { - /(.*?)\s/; - my $k = $1; - my $h = $_; - my $seq = readline(R1); - my $qual = readline(R1); - $qual .= readline(R1); - if (length($seq) > $min) { - $hsh{$k} = $h . $seq . $qual; - } - else { -# print STDERR "$h$seq too short\n"; sleep 1; - } -} -close R1; - -open R2, "<$r2"; -open O1, ">$o1"; -open O2, ">$o2"; - -while (<R2>) { - /(.*?)\s/; - my $k = $1; - my $h = $_; - my $seq = readline(R2); - my $qual = readline(R2); - $qual .= readline(R2); - if (length($seq) > $min) { - } - else { -# print STDERR "$h$seq too short\n"; sleep 1; - next; - } - if (exists($hsh{$k})) { - print O1 $hsh{$k}; - print O2 $h . $seq . $qual; - } - else { -# print STDERR "$k is missing\n"; sleep 1; - } -} -close R2; -close O1; -close O2;
--- a/falco/misc/perAmpliconAnalysis.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,354 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my $bam = shift; -my $ref = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/ref/hg19/bwa-5/hg19.fa"; -my $manifest = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; -my $base = shift || "output"; -my $samtools = shift || "/gsdata/tmp/TSACP/ampliconPipeLine/bin/samtools/samtools-0.1.18/samtools"; -my $fai = $ref . ".fai"; - -open FAI, "<$fai"; -my %idx = (); -print STDERR "Reading fa index ... "; -while (<FAI>) { - chomp; - my @row = split(/\t/, $_); - $idx{$row[0]} = [@row]; -} -print STDERR "done\n"; - -close FAI; -open REF, "<$ref"; - -my %stats = (); -my %manif = (); -my %targets = (); -my %probe = (); -my %hash = (); - -open M, "<$manifest" or die "Unable to open manifest: $manifest\n" ; -while (<M>) { last if (/\[Probes\]/) } -readline(M); -while (<M>) { - chomp; - if (/\[Targets\]/) { - my $h = readline M; - chomp $h; - my @H = split(/\t/, $h); - last; - } - my @row = split(/\t/, $_); - $probe{$row[2]}{probe} = [@row]; - $probe{$row[2]}{ULSO} = $row[9]; - $probe{$row[2]}{DLSO} = $row[11]; -} - -while (<M>) { - chomp; - s/\s+$//; - my @row = split(/\t/, $_); - push @{$targets{$row[3]}{$_}}, $row[0] foreach ($row[4] .. $row[5]); - # $manif{$aTarget} = [@row]; - my $aTarget = $row[0] . "-" . $row[3] . ":". "$row[4]-$row[5]"; - if (not exists($stats{$aTarget}{target})) { - $stats{$aTarget}{target} = [@row]; - $stats{$aTarget}{ln} = $row[5] - $row[4] + 1; - $stats{$aTarget}{n} = 0; - $stats{$aTarget}{sam} = []; - $stats{$aTarget}{depth} = 0; - $stats{$aTarget}{covs} = []; - $stats{$aTarget}{chr} = $row[3]; - $stats{$aTarget}{start} = $row[4]; - $stats{$aTarget}{end} = $row[5]; - $stats{$aTarget}{ULSO} = $probe{$row[0]}{ULSO}; - $stats{$aTarget}{DLSO} = $probe{$row[0]}{DLSO}; - $stats{$aTarget}{assayStart} = $row[4] + length($probe{$row[0]}{ULSO}); - $stats{$aTarget}{assayEnd} = $row[5] - length($probe{$row[0]}{DLSO}); - } -# print $row[0] . "\n"; - foreach my $i (0 .. 5) { - foreach my $j (0 .. 5) { -# print $row[4] + $i .":". ($row[5] - $row[4] + $j) .":". $row[0] . "\n"; -# print $row[4] + $i .":". ($row[5] - $row[4] - $j) .":". $row[0] . "\n"; -# print $row[4] - $i .":". ($row[5] - $row[4] + $j) .":". $row[0] . "\n"; -# print $row[4] - $i .":". ($row[5] - $row[4] - $j) .":". $row[0] . "\n"; - $hash{$row[3]}{$row[4] + $i}{$row[5] - $row[4] + $j} = $aTarget; - $hash{$row[3]}{$row[4] + $i}{$row[5] - $row[4] - $j} = $aTarget; - $hash{$row[3]}{$row[4] - $i}{$row[5] - $row[4] + $j} = $aTarget; - $hash{$row[3]}{$row[4] - $i}{$row[5] - $row[4] - $j} = $aTarget; - } - } -# sleep 1; -} -close M; - -# samtools view -b 25MUT5.bam chr9:133738302-133738491 | samtools calmd - /gsdata/tmp/TSACP/ampliconPipeLine/ref/hg19/bwa-5/hg19.fa | head - -#foreach my $amp (keys(%stats)) { - -# print $amp . "\n"; -# my @SAM = (); - # Fetch reads -# my $coord = $stats{$amp}{chr} .":".$stats{$amp}{start}."-".$stats{$amp}{end}; -# my $ln = $stats{$amp}{ln}; -# print $coord . " $ln\n"; - -# Open output -open QC, ">$base.qc.ann.txt"; -open QC2, ">$base.qc2.ann.txt"; -open TARGET, ">$base.qc.targets.txt"; - -#TODO Remove stampy check -my $stampy = 0; -open SAMH, "$samtools view -H $bam |"; -while (<SAMH>) { - $stampy = 1 if (/PN:stampy/); - print STDERR "STAMPY SPOTTED!!!" if (/PN:stampy/); -} -close SAMH; - -open SAM, "$samtools view $bam |"; -#open SAM, "$samtools view -b $bam | $samtools calmd - $ref |"; -# open SAM, "$samtools view -b $bam $coord | $samtools calmd - $ref |"; -while (<SAM>) { - last unless (/^@/); -} -my $cnt = 0; -my %hsh = (); -my $pamp = "."; - -#Print header - -print QC "#" . join("\t", qw/chr pos amp dp ntRef ntVar nRef nVar nA nC nG nT nN ins del/) . "\n"; -print QC2 "#" . join("\t", qw/read chr pos amp event/) . "\n"; -print TARGET "#" . join("\t", qw/amp chr start end assayStart assayEnd depth/) . "\n"; -while (<SAM>) { - # Skip stampy reads? Nope, stampy is no longer needed - #TODO Remove stampy check -# next if ($stampy == 1 && ! /XP:Z:BWA/); - chomp; - my @row = split(/\t/, $_); - my $l = 0; - my $cig = $row[5]; - $cig =~ s/(\d+)[MD]/$l+=$1/eg; - - my $amp = $hash{$row[2]}{$row[3]}{$l} || next; - #print "$row[2] $row[3] $l $amp\n"; - - push @{$stats{$amp}{sam}}, [@row]; - $stats{$amp}{depth}++; - if (($pamp ne ".") && ($amp ne $pamp)) { - print STDERR "Flushing $pamp $stats{$pamp}{depth}\n"; -# print TARGET join("\t", $pamp, map { $stats{$pamp}{$_} } qw/chr start end assayStart assayEnd depth/) . "\n"; - my $data = &call($stats{$pamp}{sam}); - &flush($data, $stats{$pamp}{chr}, $pamp, $stats{$pamp}{assayStart}, $stats{$pamp}{assayEnd}); - $stats{$pamp}{sam} = []; - } - $pamp = $amp; - $cnt++; -} - -close QC; -close QC2; -foreach my $pamp (keys %stats) { - print TARGET join("\t", $pamp, map { $stats{$pamp}{$_} || "NA"} qw/chr start end assayStart assayEnd depth/) . "\n"; -} -close TARGET; - - -# print join("\n", map {$hsh{$_} . ":" . $_} keys(%hsh)) . "\n"; -# print $cnt . "\n"; sleep 1; - close SAM; -# $stats{$amp}{depth} = $cnt; -# my $data = &call(\@SAM); -# &flush($data, $stats{$amp}{chr}, $amp); - -#} - -#foreach my $amp (keys(%stats)) { - -# print $amp . ":" . scalar(@{$stats{$amp}{sam}}) . "\n"; -#} - -sub call { - my $SAM = shift; - - my $ppos = 0; - my $pchr = ""; - my %data = (); - my $refSeq = ""; - my $c = 0; - my $col_chr = 2; - my $col_read = 9; - my $col_qual = 10; - my $col_pos = 3; - my $col_cigar = 5; - my $refSeqPad = "P"; - my %cooc = (); - my $cnt = 1; - foreach my $r (0 .. $#$SAM) { - my @row = @{$SAM->[$r]}; - my $read = $row[$col_read]; - my $qual = $row[$col_qual]; - my $pos = $row[$col_pos]; - my @cig = (); - my $aln = 0; - while ($row[$col_cigar] =~ /(\d+)(\D)/g) { - push @cig, [$1, $2]; - $aln += $1; - } - if ($ppos != $pos) { - my $offset = $idx{$row[$col_chr]}->[2]; - my $nl = int (($row[$col_pos] - 1) / $idx{$row[$col_chr]}->[3]); - $offset += $row[$col_pos] + $nl - 1; - seek REF, $offset, 0; - $refSeqPad = substr($refSeq, -1, 1); - read REF, $refSeq, 1000;# length($read) * 5; - $refSeq =~ s/\s//g; - $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. $aln); - $ppos = $pos; - } - - foreach my $cigE (@cig) { - my $n = $cigE->[0]; - if ($cigE->[1] eq "I") { - my $rpos = $pos - $row[$col_pos]; - my $insert = substr($refSeq, $rpos - 1, 1) or print STDERR "Outside?" . $rpos . ":" . length($refSeq) . " $pos\n"; - $insert .= substr($read, 0, $n, ""); - my $qinsert .= substr($qual, 0, $n, ""); - push @{$data{$row[$col_chr]}{$pos - 1}{"IR"}{$insert}}, $r; - $data{$row[$col_chr]}{$pos - 1}{"I"}{$insert}++; -# push @{$cooc{$pos - 1 }{$insert}}, $cnt; - # $cooc{($pos - 1) .":".$insert}{$cnt} = 0; - } - elsif ($cigE->[1] eq "M") { - my $mseq = substr($read, 0, $n, ""); - my $mqual = substr($qual, 0, $n, ""); - foreach my $nt (0 .. (length($mseq) - 1)) { - $data{$row[$col_chr]}{$pos + $nt}{"DP"}++; - my $ntq = substr($mqual, $nt, 1); - my $ntn = substr($mseq, $nt, 1); - if (ord($ntq) - 33 < 30) { - $ntn = "N"; - } - $data{$row[$col_chr]}{$pos + $nt}{"NT"}{$ntn}++; - push @{$data{$row[$col_chr]}{$pos + $nt}{"NTR"}{$ntn}}, $r if (uc($ntn) ne uc($data{$row[$col_chr]}{$pos + $nt}{refNT})); -# if (($ntn ne $data{$row[$col_chr]}{$pos + $nt}{"refNT"}) && ($ntn ne "N")) { - #push @{$cooc{$pos + $nt}{$ntn}}, $cnt; - # $cooc{($pos + $nt) .":".$ntn}{$cnt} = 0; -# } - } - $pos += $n; - - } - elsif ($cigE->[1] eq "D") { - my $rpos = $pos - $row[$col_pos]; - my $deletion = substr($refSeq, $rpos - 1, $n + 1); # Substring out of string error ? - push @{$data{$row[$col_chr]}{$pos - 1}{"DR"}{$deletion}}, $r; - $data{$row[$col_chr]}{$pos - 1}{"D"}{$deletion}++; - #push @{$cooc{$pos - 1 }{$deletion}}, $cnt; - # $cooc{($pos - 1) . ":" . $deletion}{$cnt} = 0; - $pos += $n; - } - } - $cnt++; - } - #my $thresh = scalar(@$SAM) * .05; - #&coocCalc(\%cooc, \%data, $thresh); - return \%data; -} - -sub coocCalc { - my $cooc = shift; - my $data = shift; - my $thresh = shift; - my %rev = (); - # Filter low frequency variants - foreach my $k (keys(%$cooc)) { - if (scalar(keys(%{$cooc->{$k}})) < $thresh) { - delete($cooc->{$k}); - next; - } - print STDERR "$k : $thresh : " . join(":", sort {$a cmp $b} keys(%{$cooc->{$k}})) . "\n"; - } - my @muts = keys(%{$cooc}); - foreach my $i (0 .. $#muts) { -# my %hsh = map { $_ => 0 } keys(%{$cooc{$muts[$i]}}); - foreach my $j (($i + 1) .. $#muts) { - my $score = 0; - foreach my $m (keys(%{$cooc->{$muts[$i]}})) { - if (exists($cooc->{$muts[$j]}{$m})) { - $score++; - } - } - print STDERR $muts[$i] .":". $muts[$j] . ":" . $score . "\n"; sleep 1; - } - } - - #{read}{mutation} - #{mutation}{read} - sleep 1; -} - -sub flush { - my $data = shift; - my $chr = shift; - my $amp = shift; - my $s = shift; - my $e = shift; - return unless (exists($data->{$chr})); - print STDERR "printing ... "; - my %reads = (); # read->pos->nt -# foreach my $p (sort {$a <=> $b} keys(%{$data->{$chr}})) { -# unless (($p >= $s) && ($p <= $e)) { -# next; -# } - foreach my $p ($s .. $e) { - my $posdat = $data->{$chr}{$p} || next; - next unless (exists($posdat->{DP})); - my $refNT = uc($posdat->{refNT}); - my @varOrd = sort { $posdat->{NT}{$b} <=> $posdat->{NT}{$a} } grep {$_ ne "N"} grep { $_ ne $refNT } keys(%{$posdat->{NT}}); - my $seqNT = join("/", @varOrd); - #my $refCNT = scalar(@{$posdat->{NT}{$refNT} || []}); - my $refCNT = $posdat->{NT}{$refNT} || 0; - my $varCNT = 0; - #$varCNT += scalar(@{$posdat->{NT}{$_}}) foreach (@varOrd); - #$varCNT += $posdat->{NT}{$_} foreach (@varOrd); - $varCNT = ($varOrd[0])?$posdat->{NT}{$varOrd[0]}:0; - my $Istr = "."; - my $Dstr = "."; - if ($varOrd[0]) { - $reads{$_}{$p} = "$refNT/$varOrd[0]" foreach (@{$posdat->{NTR}{$varOrd[0]}}); - } - if (exists($posdat->{I})) { - $Istr = join("|", map { $_ . ":" . $posdat->{I}{$_} } keys(%{$posdat->{I}})); - foreach my $I (keys(%{$posdat->{IR}})) { - $reads{$_}{$p} = "$refNT/$I" foreach (@{$posdat->{IR}{$I}}); - } - } - if (exists($posdat->{D})) { - $Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})); - foreach my $D (keys(%{$posdat->{DR}})) { - $reads{$_}{$p} = "$D/$refNT" foreach (@{$posdat->{DR}{$D}}); - } - } - #$Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})) if exists($posdat->{D}); - print QC join("\t", $chr, $p, $amp, - $posdat->{DP} || 0, - $posdat->{refNT} || ".", - $seqNT || ".", - $refCNT, $varCNT, - #(map { scalar(@{$posdat->{NT}{$_} || []})} qw(A C G T N)), $Istr, $Dstr, - (map { $posdat->{NT}{$_} || 0 } qw(A C G T N)), $Istr, $Dstr, - ) . "\n"; - # delete $data->{$chr}{$p}; - } - delete $data->{$chr}; - foreach my $r (sort { $a <=> $b } keys(%reads)) { - print QC2 join("\t", $r, $chr, $_, $amp, $reads{$r}{$_}) . "\n" foreach (sort {$a <=> $b} keys(%{$reads{$r}})); - } - print STDERR "done\n"; -} -
--- a/falco/misc/pileup2cov.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -#!/usr/bin/perl -w -# - -use strict; - -my $ref = shift; -my $targets = shift; -my $fai = $ref . ".fai"; -my %idx = (); -$| = 1; -open FAI, "<$fai"; - -print STDERR "Reading fa index ... "; -while (<FAI>) { - chomp; - my @row = split(/\t/, $_); - $idx{$row[0]} = [@row]; -} -print STDERR "done\n"; - -close FAI; - -# Read in targets and only process alignemts if start or end is within 5bp of the primer start. -my %primes = (); -open T, "<$targets"; -while (<T>) { - my @row = split(/\t/, $_); - #456 - $primes{"$row[4]" . $_} = $row[0] foreach (($row[5] - 5) .. ($row[5] + 5), ($row[6] - 5) .. ($row[6] + 5)); -} -close T; - -open REF, "<$ref"; - -my $ppos = 0; -my $pchr = ""; -my %data = (); -my $refSeq = ""; -my $c = 0; -my $col_chr = 2; -my $col_read = 9; -my $col_qual = 10; -my $col_pos = 3; -my $col_cigar = 5; -my $refSeqPad = "P"; - -my $cnt = 1; -while (<STDIN>) { - - # Skip stampy reads? - next unless (/XP:Z:BWA/); - - my @row = split(/\t/, $_); -# print STDERR $row[$col_pos] . "\n"; -# my $aln = ""; - if (($pchr ne $row[$col_chr])) { # flush data when chr changes or when target changes? - &flush(\%data, $pchr); - $pchr = $row[$col_chr]; - last if ($pchr eq "*"); - print STDERR "$pchr - Processing ... "; - } - my $read = $row[$col_read]; - my $qual = $row[$col_qual]; - my $pos = $row[$col_pos]; - my @cig = (); - my $aln = 0; - while ($row[$col_cigar] =~ /(\d+)(\D)/g) { - push @cig, [$1, $2]; - $aln += $1; - } - if ($ppos != $pos) { - my $offset = $idx{$row[$col_chr]}->[2]; - my $nl = int (($row[$col_pos] - 1) / $idx{$row[$col_chr]}->[3]); - $offset += $row[$col_pos] + $nl - 1; - seek REF, $offset, 0; - $refSeqPad = substr($refSeq, -1, 1); - read REF, $refSeq, 1000; # length($read) * 5; - $refSeq =~ s/\s//g; -# $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. (length($refSeq) - 1)); - $data{$row[$col_chr]}{$row[$col_pos] + $_}{"refNT"} = substr($refSeq, $_, 1) foreach (0 .. $aln); - $ppos = $pos; - } -# while ($row[$col_cigar] =~ /(\d+)(\D)/g) { - foreach my $cigE (@cig) { - my $n = $cigE->[0]; - if ($cigE->[1] eq "I") { -# my $insert = substr($read, 0, $1, ""); -# $data{$row[$col_chr]}{$pos}{"I"}{$insert}++; - my $rpos = $pos - $row[$col_pos]; - my $insert = substr($refSeq, $rpos - 1, 1) or print STDERR "Outside?" . $rpos . ":" . length($refSeq) . " $pos\n"; - $insert .= substr($read, 0, $n, ""); - my $qinsert .= substr($qual, 0, $n, ""); - $data{$row[$col_chr]}{$pos - 1}{"I"}{$insert}++; -# print STDERR "+"; - } - elsif ($cigE->[1] eq "M") { - my $mseq = substr($read, 0, $n, ""); - my $mqual = substr($qual, 0, $n, ""); - foreach my $nt (0 .. (length($mseq) - 1)) { - $data{$row[$col_chr]}{$pos + $nt}{"DP"}++; - my $ntq = substr($mqual, $nt, 1); - # TODO Changed from scalar to an array -# push @{$data{$row[$col_chr]}{$pos + $nt}{"NT"}{substr($mseq, $nt, 1)}}, $ntq; - $data{$row[$col_chr]}{$pos + $nt}{"NT"}{substr($mseq, $nt, 1)}++; -# print STDERR join(":", $row[$col_chr], $pos, $nt, substr($mseq, $nt, 1)) . "\n"; sleep 1; - } - $pos += $n; -# print STDERR "M"; - - } - elsif ($cigE->[1] eq "D") { -# my $rpos = $pos - $row[$col_pos]; -# my $deletion = substr($refSeq, $rpos, $1); # Substring out of string error ? -# $data{$row[$col_chr]}{$pos}{"D"}{$deletion}++; -# $pos += $1; - my $rpos = $pos - $row[$col_pos]; - my $deletion = substr($refSeq, $rpos - 1, $n + 1); # Substring out of string error ? - $data{$row[$col_chr]}{$pos - 1}{"D"}{$deletion}++; - $pos += $n; -# print STDERR "-"; - } - } -} -&flush(\%data, $pchr); - -close REF; - -sub match { - my $ref = shift; - my $seq = shift; - my $k = 5; - my $p = 0; - my @mm = (); - while (my $r = substr($$ref, $p, $k)) { - my $s = substr($$seq, $p, $k); - if ($r ne $s) { -# my $aln = ""; -# print "Mismatch!\n"; - foreach my $i (0 .. $k - 1) { - if (substr($r, $i, 1) ne substr($s, $i, 1)) { -# $aln .= "x"; - push @mm, [$p + $i, substr($r, $i, 1), substr($s, $i, 1)]; - } - else { -# $aln .= "|"; - } - } -# print $r . "\n$aln\n" . $s . "\n"; - - } - else { -# print $r . "\n" . $s . "\n"; - } - $p += $k; - } - - return \@mm; -} - -sub flush { - my $data = shift; - my $chr = shift; - return unless (exists($data->{$chr})); - print STDERR "printing ... "; - foreach my $p (sort {$a <=> $b} keys(%{$data->{$chr}})) { - my $posdat = $data->{$chr}{$p} || next; - next unless (exists($posdat->{DP})); - my $refNT = uc($posdat->{refNT}); - my @varOrd = sort { $posdat->{NT}{$b} <=> $posdat->{NT}{$a} } grep { $_ ne $refNT } keys(%{$posdat->{NT}}); - my $seqNT = join("/", @varOrd); - #my $refCNT = scalar(@{$posdat->{NT}{$refNT} || []}); - my $refCNT = $posdat->{NT}{$refNT} || 0; - my $varCNT = 0; - #$varCNT += scalar(@{$posdat->{NT}{$_}}) foreach (@varOrd); - $varCNT += $posdat->{NT}{$_} foreach (@varOrd); - my $Istr = "."; - my $Dstr = "."; - $Istr = join("|", map { $_ . ":" . $posdat->{I}{$_} } keys(%{$posdat->{I}})) if exists($posdat->{I}); - $Dstr = join("|", map { $_ . ":" . $posdat->{D}{$_} } keys(%{$posdat->{D}})) if exists($posdat->{D}); - print join("\t", $chr, $p, - $posdat->{DP} || 0, - $posdat->{refNT} || ".", - $seqNT || ".", - $refCNT, $varCNT, - #(map { scalar(@{$posdat->{NT}{$_} || []})} qw(A C G T N)), $Istr, $Dstr, - (map { $posdat->{NT}{$_} || 0 } qw(A C G T N)), $Istr, $Dstr, - ) . "\n"; -# delete $data->{$chr}{$p}; - } - delete $data->{$chr}; - print STDERR "done\n"; -}
--- a/falco/misc/plots.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -#!/usr/bin/Rscript - -args <- commandArgs(T) -print(args[1]) -print(args[2]) -print(args[3]) - -read.delim(args[2], header=F, stringsAsFactors=F) -> qc -read.delim(args[1], header=F, stringsAsFactors=F) -> d - -#unique(unlist(strsplit(d$V3, "\\|"))) -> targets -targets <- qc$V1 -d[,7]/d[,4] * 100 -> d$pctREF -d[,8]/d[,4] * 100 -> d$pctVAR - -pdf(args[3], width=14) -for (i in targets) { - sel <- grepl(i, d$V3) - print(i) - for (c in unique(d$V1[sel])) { - csel <- d$V1 == c - print(c) - reg <- paste(range(d$V2[sel & csel]), collapse="-", sep="-") - creg <- paste(c, reg, sep=":") - print(reg) - print(creg) - plot(d[sel & csel,c(2,4)], type="l", ylim=c(0,max(d[sel & csel,4])), main=paste(i, creg, sep=" "), xlab="position", ylab="depth") - lines(d[sel & csel,c(2,7)], type="l", col=4) - lines(d[sel & csel,c(2,8)], type="l", col=2) - limP <- range(d[sel & csel,2]) - abline(v=c(limP[1], limP[1] + 150, limP[2] - 150, limP[2]),lty=4) - - plot(d[sel & csel,2], d$pctREF[sel & csel], type="l", ylim=c(0,100), main=paste(i, creg, sep=" "), xlab="position", ylab="%") - lines(d[sel & csel,2], d$pctVAR[sel & csel], type="l", col=2) - abline(h=c(1,5,10,50,90,95,99), lty=3, col=1) - abline(v=c(limP[1], limP[1] + 150, limP[2] - 150, limP[2]),lty=4) - } -} -hist(d$pctVAR[d$pctVAR < 20], breaks=40, ylim=c(0,1000)) -hist(d$pctREF[d$pctREF > 80], breaks=40, ylim=c(0,1000)) - -dev.off() - -print(summary(d$pctVAR)) - -
--- a/falco/misc/plotsPng.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,502 +0,0 @@ -#!/usr/bin/Rscript - -args <- commandArgs(T) - -print(args[1]) # qc.ann.qual.txt -print(args[2]) # qc2.ann.qtxt -print(args[3]) # qc.targets.txt -print(args[4]) # res.txt (unfiltered) -print(args[5]) # clinvar -print(args[6]) # lociFilt -print(args[7]) # basename -options(warn=1) -print(paste("Reading", args[1], sep=" ")); -read.delim(args[1], header=T, stringsAsFactors=F) -> d -print(paste("Reading", args[2], sep=" ")); -read.delim(args[2], header=T, stringsAsFactors=F) -> d2 -print(paste("Reading", args[3], sep=" ")); -read.delim(args[3], header=T, stringsAsFactors=F) -> qc -print(paste("Reading", args[4], sep=" ")); -read.delim(args[4], header=T, stringsAsFactors=F, row.names=NULL) -> res -print(paste("Reading", args[5], sep=" ")); -read.delim(args[5], header=T, stringsAsFactors=F) -> dclin -print(paste("Reading", args[6], sep=" ")); -read.delim(args[6], header=F, stringsAsFactors=F) -> lociFilt -base <- args[7] - -# Error rate per cycle -# VAF distribution -# varDepth distribution ? -# Print coverage plots per amplicon - -tmpCP <- paste(d$X.chr, d$pos, sep=":") -tmpClin <- paste(dclin$X.chr, dclin$pos, sep=":") -tmpSnp <- paste(paste("chr", lociFilt[,1], sep=""), lociFilt[,2], sep=":") - -inClin <- tmpCP %in% tmpClin - -inSnp <- tmpCP %in% tmpSnp - -dir.create(base) -setwd(base) -#unique(unlist(strsplit(d$V3, "\\|"))) -> targets -targets <- qc[,1] -if (1) { -print("Plotting variant heatmap") -# Including off targets increases the amplicon length set at median amplicon length + 10%. -median(qc$end - qc$start) -> maxAmpLn -maxAmpLn <- ceiling(1.2 * maxAmpLn) -print(maxAmpLn) -ampHeatF <- matrix(ncol=maxAmpLn, nrow=nrow(qc)) -ampHeatR <- matrix(ncol=maxAmpLn, nrow=nrow(qc)) -#dPos <- paste(d$chr, d$pos, sep=":") -#errPos <- paste(dclin$chr, dclin$pos, sep=":") -#dPosClin <- dPos %in% errPos - -dPosClin <- !inClin & !inSnp - -for (i in 1:nrow(qc)) { - d$pos %in% qc$start[i]:qc$end[i] -> sel - poss <- d$pos[sel & !dPosClin] - qc$start[i] + 1 - poss <- poss[poss <= maxAmpLn] - ampHeatF[i, poss] <- d$nVar[sel & !dPosClin] + d$nN[sel & !dPosClin] - ampHeatR[i, poss] <- rev(d$nVar[sel & !dPosClin] + d$nN[sel & !dPosClin]) -} -png(paste(base,"heat","png", sep="."), width=960, height=480) -par(mar=c(4,4,4,2) + .1) - -ampHeatF[is.na(ampHeatF)] <- 0 -ampHeatR[is.na(ampHeatR)] <- 0 -layout(matrix(1:2, nrow=2)) -maxN <- quantile(ampHeatF, .99) -#heatmap(ampHeat) -boxplot(ampHeatF, ylim=c(0, maxN), pch=20, cex=.4, main="Non reference counts R1") -rect(150, 0, ncol(ampHeatF), maxN, col="#00000040") -boxplot(ampHeatR, ylim=c(0, maxN), pch=20, cex=.4, main="Non reference counts R2") -rect(150, 0, ncol(ampHeatR), maxN, col="#00000040") -dev.off() - -#d[,7]/d[,4] * 100 -> d$pctREF -#d[,8]/d[,4] * 100 -> d$pctVAR -d$nRef/d$dp * 100 -> d$pctREF -d$nVar/d$dp * 100 -> d$pctVAR -d$vaf <- d$nVar / (d$nVar + d$nRef) * 100 -print("Plotting ref frequencies") -png(paste(base,"raf","png", sep="."), width=480, height=480) -dref <- density(d$pctREF[!dPosClin]) -#plot(dref, ylim=range(dref$y[dref$x < 80] )) -hist(d$pctREF[!dPosClin], breaks=100, ylim=c(0, 30), col="#00000040", border=NA) -dev.off() - -print("Plotting var frequencies") -png(paste(base,"vaf","png", sep="."), width=480, height=480) -dvar <- density(d$pctVAR[!dPosClin]) -#plot(dvar, ylim=range(dvar$y[dvar$x > 20] )) -hist(d$pctVAR[!dPosClin], breaks=100, ylim=c(0, 30), col="#00000040", border=NA) -dev.off() - -# Set vaf cutoff -#q95 <- quantile(d$qScore, .95, na.rm=T) -q95 <- 20 -vs95 <- sd(d$pctVAR[!dPosClin & d$qScore < q95], na.rm=T) -v95 <- mean(d$pctVAR[!dPosClin & d$qScore < q95], na.rm=T) + vs95 * 3 - -nCall <- sum((d$pctVAR > v95) & d$qScore > q95 & !inSnp, na.rm=T) -print(nCall) -print("Plotting vaf vs q") -png(paste(base,"snv-q","png", sep="."), width=480, height=480) -plot(d$qScore, d$pctVAR, pch=20, cex=.5, main=paste("q:", q95, "-", "v:", v95, "--", "s:", nCall, sep=" ")) -abline(h=c(1,5), v=c(20,13), lty=2) -abline(v=q95, h=v95, lty=3, col=2) -points(d$qScore[d$dp < 100], d$pctVAR[d$dp < 100], pch=20, cex=1.2, col=2) -points(d$qScore[d$nVar < 10], d$pctVAR[d$nVar < 10], pch=20, cex=1, col=4) -legend(30,80, c("pass", "dp < 100", "nVar < 10"), col=c(1,2,4), pch=20) -dev.off() - -print("Plotting vaf vs q zoomed") -png(paste(base,"snv-q-zoom","png", sep="."), width=480, height=480) -plot(d$qScore, d$pctVAR, pch=20, cex=.5, xlim=c(0, 40),ylim=c(0,10)) -abline(h=c(1,5), v=c(20,13), lty=2) -abline(v=q95, h=v95, lty=3, col=2) -points(d$qScore[d$dp < 100], d$pctVAR[d$dp < 100], pch=20, cex=1.2, col=2) -points(d$qScore[d$nVar < 10], d$pctVAR[d$nVar < 10], pch=20, cex=1, col=4) -legend("topright", c("pass", "dp < 100", "nVar < 10"), col=c(1,2,4), pch=20) -dev.off() - -print("Plotting ins vs q") -d$vafI <- 0 -d$occI <- 0 -if (sum(d$ins != ".") > 0) { -png(paste(base,"ins-q","png", sep="."), width=480, height=480) -data.frame(matrix(unlist(strsplit(unlist(strsplit(as.character(d$ins[d$ins != "."]), "\\|")), ":")), ncol=2, byrow=T)) -> insDat -colnames(insDat) <- c("seq", "occ") -insDat$seq <- as.character(insDat$seq) -insDat$occ <- as.numeric(as.vector(insDat$occ)) -nchar(insDat$seq) -> insDat$ln -d$occI[d$ins != "."] <- insDat$occ -d$vafI[d$ins != "."] <- insDat$occ / d$nRef[d$ins != "."] -d$qScoreI[d$qScoreI > 1000] <- 1000 -plot(d$qScoreI, d$occI, pch=20, cex=1) -abline(h=c(10), v=c(20,13), lty=2) -# dp 500 -sel <- d$dp < 100 -points(d$qScoreI[sel], d$occI[sel], pch=20, cex=1.2, col=2) -# nVar 10 -#sel <- d$occI < 10 -#points(d$qScoreI[sel], d$occI[sel], pch=20, cex=1, col=3) -# vaf < 0.01 -sel <- d$vafI < 0.01 -points(d$qScoreI[sel], d$occI[sel], pch=20, cex=1, col=4) -legend("topleft", c("pass", "dp < 100", "vaf < 0.01"), col=c(1,2,4), pch=20) -dev.off() -} - -print("Plotting del vs q") -d$vafD <- 0 -d$occD <- 0 -if (sum(d$del != "." ) > 0) { -png(paste(base,"del-q","png", sep="."), width=480, height=480) -data.frame(matrix(unlist(strsplit(unlist(strsplit(as.character(d$del[d$del != "."]), "\\|")), ":")), ncol=2, byrow=T)) -> delDat -colnames(delDat) <- c("seq", "occ") -delDat$seq <- as.character(delDat$seq) -delDat$occ <- as.numeric(as.vector(delDat$occ)) -nchar(delDat$seq) -> delDat$ln -d$occD[d$del != "."] <- delDat$occ -d$vafD[d$del != "."] <- d$occD[d$del != "."] / d$nRef[d$del != "."] -d$qScoreD[d$qScoreD > 1000] <- 1000 -#hist(d$qScoreD, breaks=1000, ylim=c(0,100)) -#print(sum(d$qScoreD > 20)) -#Sys.sleep(1) -plot(d$qScoreD, d$occD, pch=20, cex=1) -abline(h=c(10), v=c(20,13), lty=2) -# dp 500 -sel <- d$dp < 100 -points(d$qScoreD[sel], d$occD[sel], pch=20, cex=1.2, col=2) -# nVar 10 -#sel <- d$occD < 10 -#points(d$qScoreD[sel], d$occD[sel], pch=20, cex=1, col=3) -# vaf < 0.01 -sel <- d$vafD < 0.01 -points(d$qScoreD[sel], d$occD[sel], pch=20, cex=1, col=4) -legend("topleft", c("pass", "dp < 100", "vaf < 0.01"), col=c(1,2,4), pch=20) -dev.off() -} - -sub("chr", "", qc$chr) -> qc$chrn -ampOrd <- order(qc$chrn, qc$start) - -print("Plotting amplicon depths") -png(paste(base,"amp-dp","png", sep="."), width=960, height=480) -barplot(qc$depth[ampOrd]) -abline(h=100, lty=2) -totRead <- sum(qc$depth, na.rm=T) -legend("topright", paste("Total read count: ", totRead, sep="")) -dev.off() -} -# -res$POS <- as.numeric(as.vector(res$POS)) -d$pos <- as.numeric(as.vector(d$pos)) - -grepl("a", d$ntRef, ignore.case=T) -> Asel -grepl("c", d$ntRef, ignore.case=T) -> Csel -grepl("g", d$ntRef, ignore.case=T) -> Gsel -grepl("t", d$ntRef, ignore.case=T) -> Tsel -cntr <- 0 - -biasTable <- data.frame(matrix(NA, nrow=length(targets), ncol=12), row.names=targets) -colnames(biasTable) <- c("AC", "AG", "AT", "CA", "CG", "CT", "GA", "GC", "GT", "TA", "TC", "TG") - -for (i in targets) { - sel <- grepl(i, d$amp) - print(i) - for (c in unique(d[sel,1])) { - csel <- d[,1] == c - print(c) - reg <- paste(range(d[sel & csel,2]), collapse="-", sep="-") - creg <- paste(c, reg, sep=":") - - qcsel <- qc[,1] == i - allsel <- sel & csel - clinSel <- dclin$amp == i - clinPos <- dclin$pos[clinSel] -# inClin <- d$pos %in% clinPos - - #dels <- (d[,15] != ".") & allsel - #ins <- (d[,14] != ".") & sel - # print(reg) - # print(creg) - - # Select annotations - # calculate quantiles and plot them -# quantile(d$pctVAR[sel & csel], c(.75,.90,.95,.99), na.rm=T) -> cutoffs - tmp <- d[sel & csel,] - #dels <- tmp[,15] != "." - #ins <- tmp[,14] != "." - dels <- allsel & d$del != "." - ins <- allsel & d$ins != "." - - resTmp <- res[(res$POS >= min(tmp[,2])) & (res$POS <= max(tmp[,2])) & (res$X.CHROM == c),] - #resSel <- res$TARGET == i - png(paste(base, i, "cov", "png", sep="."), width=960, height=480) - - xvec <- c(0, rep(1:(sum(allsel) - 1), each=2), sum(allsel)) - layout(matrix(1:2, ncol=1), heights=c(2,1)) - par(mar=c(0, 4, 4, 7) + .1, xaxt="n") - print("Cov") - plot(NULL, type="n", main=i, xlab="Position", ylab="Depth", xlim=range(d$pos[allsel]), ylim=range(0, d$dp[allsel])) - xvec <- d$pos[allsel] - yvec <- d$dp[allsel] - - polygon(rep(c(xvec, max(xvec) + 1), each=2) - .5, c(0, rep(yvec, each=2), 0), col="#00000010", border=1) - polygon(rep(c(xvec, max(xvec) + 1), each=2) - .5, c(0, rep(rowSums(d[allsel, 7:8]), each=2), 0), col="#00000010") -# polygon(rep(c(xvec, max(xvec) + 1), each=2) - .5, c(0, rep(d$nVar[allsel], each=2), 0), col=2) - varCol <- rep(2, sum(allsel)) - varCol[grepl("^a", d$ntVar[allsel], ignore.case=T)] <- "green" - varCol[grepl("^c", d$ntVar[allsel], ignore.case=T)] <- "blue" - varCol[grepl("^g", d$ntVar[allsel], ignore.case=T)] <- "black" - varCol[grepl("^t", d$ntVar[allsel], ignore.case=T)] <- "red" - rect(xvec-.5,d$nVar[allsel],xvec+.5,0, col=varCol) - - - ampMax <- max(d[allsel,4]) - #abline(v=resTmp$POS, lty=2, col=2) - #delMark <- list() - #insMark <- list() - - for (idx in which(dels)) { - matrix(unlist(strsplit(as.character(as.vector(d[idx,15])), "[:|]")), ncol=2, byrow=T) -> delDat - nchar(delDat[,1]) -> lngts - dpths <- as.numeric(delDat[,2]) - x1 <- d[idx,2] + .5 - x2 <- x1 + lngts - 1 - if (x2 > max(d$pos[allsel])) { - next - } - # delMark[[length(delMark) + 1]] <- c(x1, x2) - rect(x1, ampMax - dpths , x2, ampMax, col="#00000040") - } - - for (idx in which(ins)) { - matrix(unlist(strsplit(as.character(as.vector(d[idx,14])), "[:|]")), ncol=2, byrow=T) -> insDat - nchar(insDat[,1]) -> lngts - dpths <- as.numeric(insDat[,2]) - x1 <- d$pos[idx] + 1 - # insMark[length(insMark) + 1] <- x1 - for (ii in 1:ncol(insDat)) { - polygon( - c(x1, x1 - (.5 * lngts[ii]), x1 + (.5 * lngts[ii])), - c(ampMax, ampMax - dpths[ii], ampMax - dpths[ii]), - , col="#00000040") - } - } - par(xpd=NA) - legend(max(d$pos[allsel]) + sum(allsel) * 0.05, ampMax, legend=c("Filtered nt", "Ref nt", "Non-ref nt"), col=c("#00000040", "#00000080", "red"), pch=15) - legend(max(d$pos[allsel]) + sum(allsel) * 0.05, 0, legend=c("A", "C", "G", "T"), col=c("green", "blue", "black", "red"), pch=15) - par(xpd=F) - par(mar=c(5, 4, 0, 7) + .1, xaxt="s") - plot(NULL, type="n", xlab="Position", ylab=NA, xlim=range(d$pos[allsel]), ylim=c(0,4.5), yaxt="n") - axis(side=2, at=1:4, labels=c("ins", "del", "snv", "ref"), las=2) - abline(h=1:4, col="#00000040") - sres <- nchar(as.character(resTmp$REF)) == nchar(as.character(resTmp$ALT)) - dres <- nchar(resTmp$REF) > nchar(resTmp$ALT) - ires <- nchar(resTmp$REF) < nchar(resTmp$ALT) - - resTmp$marks <- rep(3.4, nrow(resTmp)) - - resTmp$cols <- rep("#00000040", nrow(resTmp)) - resTmp$cols[grepl("^a", resTmp$ALT, ignore.case=T) & sres] <- "green" - resTmp$cols[grepl("^c", resTmp$ALT, ignore.case=T) & sres] <- "blue" - resTmp$cols[grepl("^g", resTmp$ALT, ignore.case=T) & sres] <- "black" - resTmp$cols[grepl("^t", resTmp$ALT, ignore.case=T) & sres] <- "red" - - #resTmp$cols[dres] <- 2 - #resTmp$cols[ires] <- 2 - resTmp$marks[dres] <- 2.4 - resTmp$marks[ires] <- 1.4 - resTmp$markP1 <- resTmp$POS -.5 - resTmp$markP2 <- resTmp$POS +.5 - resTmp$markP1[dres] <- resTmp$POS[dres] +.5 - resTmp$markP2[dres] <- resTmp$POS[dres] +.5 + nchar(resTmp$REF[dres]) - 1 - resTmp$markP1[ires] <- resTmp$POS[ires] +.5 - resTmp$markP2[ires] <- resTmp$POS[ires] +.5 + 1 - ntCol <- rep(1, sum(allsel)) - ntCol[grepl("a", d$ntRef[allsel], ignore.case=T)] <- "green" - ntCol[grepl("c", d$ntRef[allsel], ignore.case=T)] <- "blue" - ntCol[grepl("g", d$ntRef[allsel], ignore.case=T)] <- "black" - ntCol[grepl("t", d$ntRef[allsel], ignore.case=T)] <- "red" - - rect(d$pos[allsel] -.5, 4.4, d$pos[allsel] +.5, 3.6, col=ntCol, border=0) - rect(resTmp$markP1, resTmp$marks, resTmp$markP2, resTmp$marks - .8, col=resTmp$cols, border=0) - - if(length(clinPos != 0)) { - rect(clinPos - .5, 3.5, clinPos + .5, .5, border="black", lwd=2) - } - #lapply(delMark, function(x) { rect(x[1], 2, x[2], 1, col=2, border=NA) }) - #lapply(insMark, function(x) { rect(x[1], 1, x[1] + 1, 0, col=3, border=NA) }) - - # Highlight clinically relevant loci - #for (i in which(dclin$amp == i)) { - # if (dclin$REF[i] == nchar - #} - - dev.off() - - sansClin <- allsel & !inClin - sansSnp <- allsel & !inSnp - - d$nA[sansClin & sansSnp & Asel] -> AA - d$nC[sansClin & sansSnp & Asel] -> AC - d$nG[sansClin & sansSnp & Asel] -> AG - d$nT[sansClin & sansSnp & Asel] -> AT - - d$nA[sansClin & sansSnp & Csel] -> CA - d$nC[sansClin & sansSnp & Csel] -> CC - d$nG[sansClin & sansSnp & Csel] -> CG - d$nT[sansClin & sansSnp & Csel] -> CT - - d$nA[sansClin & sansSnp & Gsel] -> GA - d$nC[sansClin & sansSnp & Gsel] -> GC - d$nG[sansClin & sansSnp & Gsel] -> GG - d$nT[sansClin & sansSnp & Gsel] -> GT - - d$nA[sansClin & sansSnp & Tsel] -> TA - d$nC[sansClin & sansSnp & Tsel] -> TC - d$nG[sansClin & sansSnp & Tsel] -> TG - d$nT[sansClin & sansSnp & Tsel] -> TT - - print("Bias") - png(paste(base, i, "bias", "png", sep="."), width=960, height=480) - - Acnt <- sum(sum(AA), sum(AC), sum(AG), sum(AT)) - Ccnt <- sum(sum(CA), sum(CC), sum(CG), sum(CT)) - Gcnt <- sum(sum(GA), sum(GC), sum(GG), sum(GT)) - Tcnt <- sum(sum(TA), sum(TC), sum(TG), sum(TT)) - - NTsums <- c( - sum(AC)/Acnt, sum(AG)/Acnt, sum(AT)/Acnt, - sum(CA)/Ccnt, sum(CG)/Ccnt, sum(CT)/Ccnt, - sum(GA)/Gcnt, sum(GC)/Gcnt, sum(GT)/Gcnt, - sum(TA)/Tcnt, sum(TC)/Tcnt, sum(TG)/Tcnt) - NTsums[!is.finite(NTsums)] <- 0 - NTsums[is.nan(NTsums)] <- 0 - NTsums[is.na(NTsums)] <- 0 - - barplot(NTsums, names.arg=c("AC", "AG", "AT", "CA", "CG", "CT", "GA", "GC", "GT", "TA", "TC", "TG"), main=i) - dev.off() - biasTable[rownames(biasTable) == i, ] <- NTsums - - print("Cov2") - png(paste(base, i, "cov2", "png", sep="."), width=960, height=480) - layout(matrix(1:2, ncol=1), heights=c(2,1)) - par(mar=c(0, 4, 4, 7) + .1, xaxt="n") - - - dat <- d2[d2$amp == i,] - rled <- rle(sort(dat$pos)) - rds <- sort(unique(dat$X.read)) - lst <- c() - for (ii in order(rled$lengths, decreasing=T)) - { - - rled$values[ii] -> pos - dat$X.read[dat$pos == pos] - lst <- c(lst, rds %in% dat$X.read[dat$pos == pos]) - - } - #xlim <- range(dat$pos) - xlim=range(d$pos[allsel]) - ylim=range(0, d$dp[allsel]) - plot(NULL, xlim=xlim, ylim=ylim, main=i, ylab="Depth") - rect(xlim[1] - 0.5, 0, xlim[2] + .5, ylim[2], col="#00000010") - if (length(lst) > 0) { - matrix(lst, nrow=length(rds), byrow=F) -> mat - do.call( order, data.frame(mat) ) -> ord - for (e in 1:length(ord)) { - sel <- dat$X.read == rds[ord[e]] - colvec <- rep(1, sum(sel)) - colvec[grepl("A$", dat$event[sel], ignore.case=T)] <- "green" - colvec[grepl("C$", dat$event[sel], ignore.case=T)] <- "blue" - colvec[grepl("G$", dat$event[sel], ignore.case=T)] <- "black" - colvec[grepl("T$", dat$event[sel], ignore.case=T)] <- "red" - #points(dat$pos[ sel ], rep(e, sum(sel)), col=colvec, pch=20, cex=.2) - segments(dat$pos[ sel ] - .5, rep(e, sum(sel)), dat$pos[ sel ] + .5, rep(e, sum(sel)), col=colvec, pch=20, cex=.2) - } - } - - par(xpd=NA) - legend(max(d$pos[allsel]) + sum(allsel) * 0.05, ampMax, legend=c("Filtered nt", "Ref nt", "Non-ref nt"), col=c("#00000040", "#00000080", "red"), pch=15) - legend(max(d$pos[allsel]) + sum(allsel) * 0.05, 0, legend=c("A", "C", "G", "T"), col=c("green", "blue", "black", "red"), pch=15) - par(xpd=F) - par(mar=c(5, 4, 0, 7) + .1, xaxt="s") - plot(NULL, type="n", xlab="Position", ylab=NA, xlim=range(d$pos[allsel]), ylim=c(0,4.5), yaxt="n") - axis(side=2, at=1:4, labels=c("ins", "del", "snv", "ref"), las=2) - abline(h=1:4, col="#00000040") - sres <- nchar(as.character(resTmp$REF)) == nchar(as.character(resTmp$ALT)) - dres <- nchar(resTmp$REF) > nchar(resTmp$ALT) - ires <- nchar(resTmp$REF) < nchar(resTmp$ALT) - - resTmp$marks <- rep(3.4, nrow(resTmp)) - - resTmp$cols <- rep("#00000040", nrow(resTmp)) - resTmp$cols[grepl("^a", resTmp$ALT, ignore.case=T) & sres] <- "green" - resTmp$cols[grepl("^c", resTmp$ALT, ignore.case=T) & sres] <- "blue" - resTmp$cols[grepl("^g", resTmp$ALT, ignore.case=T) & sres] <- "black" - resTmp$cols[grepl("^t", resTmp$ALT, ignore.case=T) & sres] <- "red" - - #resTmp$cols[dres] <- 2 - #resTmp$cols[ires] <- 2 - resTmp$marks[dres] <- 2.4 - resTmp$marks[ires] <- 1.4 - resTmp$markP1 <- resTmp$POS -.5 - resTmp$markP2 <- resTmp$POS +.5 - resTmp$markP1[dres] <- resTmp$POS[dres] +.5 - resTmp$markP2[dres] <- resTmp$POS[dres] +.5 + nchar(resTmp$REF[dres]) - 1 - resTmp$markP1[ires] <- resTmp$POS[ires] +.5 - resTmp$markP2[ires] <- resTmp$POS[ires] +.5 + 1 - ntCol <- rep(1, sum(allsel)) - ntCol[grepl("a", d$ntRef[allsel], ignore.case=T)] <- "green" - ntCol[grepl("c", d$ntRef[allsel], ignore.case=T)] <- "blue" - ntCol[grepl("g", d$ntRef[allsel], ignore.case=T)] <- "black" - ntCol[grepl("t", d$ntRef[allsel], ignore.case=T)] <- "red" - - rect(d$pos[allsel] -.5, 4.4, d$pos[allsel] +.5, 3.6, col=ntCol, border=0) - rect(resTmp$markP1, resTmp$marks, resTmp$markP2, resTmp$marks - .8, col=resTmp$cols, border=0) - - if(length(clinPos != 0)) { - rect(clinPos - .5, 3.5, clinPos + .5, .5, border="black", lwd=2) - } - - - dev.off() - -# png(paste(base, i, "vaf", "png", sep="."), width=960, height=480) -# plot(d[sel & csel,2], d$vaf[sel & csel], type="l", ylim=c(0,100), main=paste(i, creg, cutoffs[3], sep=" "), xlab="position", ylab="%", col=2) - #lines(d[sel & csel,2], d$pctVAR[sel & csel], type="l", col=2) -# abline(h=100) -# abline(h=c(1,5,10,50,90,95,99), lty=3, col=1) -# abline(h=cutoffs[3], lty=4, col=2) -# abline(v=c(limP[1], limP[1] + 150, limP[2] - 150, limP[2]),lty=4) -# abline(v=c(qc[qcsel,8:9]), lty=5, col=2) -# if (length(labs != 0)) { -# text(resTmp$POS[resTmp$vaf > (cutoffs[3]/100)], 50, labels=resTmp$Amino_Acid_change[resTmp$vaf > (cutoffs[3]/100)]) -# abline(v=resTmp$POS[resTmp$vaf > (cutoffs[3]/100)], col="grey", lty=4) -# } -# dev.off() - } -} - -png(paste(base, "biasheat", "png", sep="."), width=960, height=960) -write.table(biasTable, paste(base, "bias", "tsv", sep="."), sep="\t") -biasTable[is.na(biasTable)] <- 0 -heatmap(data.matrix(biasTable), Colv=NA, scale="r") -dev.off() -png(paste(base, "bias", "png", sep="."), width=960, height=480) -boxplot(data.matrix(biasTable), pch=20, cex=.5) -dev.off() -warnings() -#hist(d$pctVAR[d$pctVAR < 20], breaks=40, ylim=c(0,1000)) -#hist(d$pctREF[d$pctREF > 80], breaks=40, ylim=c(0,1000)) - -#print(summary(d$pctVAR)) - -
--- a/falco/misc/plotsQC.R Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -#!/usr/bin/Rscript - -args <- commandArgs(T) -print(args[1]) -print(args[2]) - -read.delim(args[1], header=F, stringsAsFactors=F) -> alnStats -read.delim(args[2], header=F, stringsAsFactors=F) -> errStats - -library(RColorBrewer) -#cols <- brewer.pal(3, "Blues") -cols <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7") - -xlegend <- 1.2 * nrow(alnStats) * 1.15 -png("alnStats.png", width=960, height=480, res=72) - -alnStats[,2:5] / 1000000 -> alnStats[,2:5] -fair <- mean(alnStats[,2]) -sub(".bam$", "", alnStats[,1]) -> alnStats[,1] -sub(".qc.ann.txt$", "", errStats[,1]) -> errStats[,1] - -oldMar <- par()$mar -par(mar=c(8.1, 4.1, 4.1, 6.1), xpd=T) -barplot(as.matrix(t(alnStats[order(alnStats[,1]),c(3:5)])), names.arg=alnStats[order(alnStats[,1]),1], las=3, col=cols[1:3], main="Alignment efficiency", ylab="Reads (Millions)", legend.text=c("Ontarget", "Offtarget", "Unmapped"), angle=.5, args.legend=c(x=xlegend)) -par(xpd=F) -abline(h=fair, lty=2) -dev.off() - -png("errStats.png", width=960, height=480, res=72) -par(mar=c(8.1, 4.1, 4.1, 6.1)) -barplot(errStats$V4[order(errStats[,1])], names.arg=errStats[order(errStats[,1]),1], las=3, col=cols[1], main="Error rate", ylab="%") - -abline(h=1, lty=2) -dev.off() - -png("qualStats.png", width=960, height=480, res=72) -par(mar=c(8.1, 4.1, 4.1, 6.1), xpd=T) -barplot(as.matrix(t(alnStats[order(alnStats[,1]),c(6:9)])), names.arg=alnStats[order(alnStats[,1]),1], las=3, col=cols[1:4], main="Quality stats", ylab="%", legend.text=c("Q > 30", "30 < Q >= 20", "20 < Q >= 10", "Q < 10"), angle=.5, args.legend=c(x=xlegend)) -dev.off() - - -#library(ggplot2) -#png("alnStatsgg.png", width=960, height=480, res=72) -#df <- data.frame( -# sample= c(rep(alnStats[,1], 3)), -# target = c(rep("ontarget", nrow(alnStats)), rep("offtarget", nrow(alnStats)), rep("unmapped", nrow(alnStats))), -# count = c(alnStats[,3], alnStats[,4], alnStats[,5]) -#) -# -#ggplot(data=df, aes(x=sample, y=count, fill=target)) + geom_bar(stat="identity") -#dev.off()
--- a/falco/misc/qc2vcf.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,135 +0,0 @@ -#!/usr/bin/perl - -use strict; - -my $qc = shift; - -my $minDp = 100; -my $minVarDp = 5; -my $minVaf = 0.01; - -my $base = (split(/\//, $qc))[-1]; -my $header = qq(##fileformat=VCFv4.1 -##FORMAT=<ID=DP,Number=1,Type=Interger,Description="Depth"> -##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele Distribution"> -##FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele Ballance nref/nref+nvar"> -##INFO=<ID=TARGET,Numer=1,Type=String,Description="TSACP Target name"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $base -); - -my $chr = 0; -my $pos = 1; -my $target = 2; -my $dp = 3; -my $ref = 4; -my $var = 5; -my $nref = 6; -my $nvar = 7; -my $nA = 8; -my $nC = 9; -my $nG = 10; -my $nT = 11; -my $nN = 12; -my $ins = 13; -my $del = 14; -my $pval = 15; -my $pvala = 16; -my $varQual = 17; -my $insQual = 18; -my $delQual = 19; - -my %acgt = (A => 0, C => 1, G => 2, T => 3); -print $header; -open QC, "<$qc"; -while (<QC>) { - chomp; - next if (/^#/); - next if (/^X\./); - my @row = split(/\t/, $_); - next if ($row[$target] eq "."); - - my $VAR = substr($row[$var], 0, 1); - my $REF = $row[$ref]; - my $nvarall = $row[$nvar]; - my $indel = $row[$ins] . $row[$del]; - if ($row[$nvar] > 0 || $indel eq "..") { - my %ord = ( A => $row[$nA], C => $row[$nC], G => $row[$nG], T => $row[$nT], N => $row[$nN] ); - $ord{uc($REF)} = -1; # Exclude ref from sort - $ord{N} = -1; # Exclude N! - my @order = sort { $ord{$b} <=> $ord{$a} } keys(%ord); - my $dpVar = $ord{$order[0]}; - my $VAR = $order[0]; - my $skip = 0; - my $tot = $row[$nref] + $dpVar; - my $vaf = ($tot > 0)?$dpVar / $tot:"NA"; # Excluding other alleles... - #$skip++ if ($tot == 0); - #$skip++ if ($ord{$order[0]} == $ord{$order[1]}); # Multiallelic, skipping for now - #$skip++ if ($dpVar == 0); # Skip if dpVar is zero, can occur when N is the only variant. Above line also protects for this. - #$skip++ if ($dpVar < $minVarDp); - #$skip++ if ($row[$dp] < $minDp); - #$skip++ if ($vaf < $minVaf); - my $gt = "$row[$ref]/$VAR"; - my $qual = $row[$varQual] || 0; - $skip++ if ($qual == 0); - my $filter = 0; - my $info = "TARGET=$row[$target]"; - my $format = "DP:AD:AB"; - my $sample = "$row[$dp]:$row[$nref],$dpVar:$vaf"; - print join("\t", @row[$chr, $pos], ".", $REF, $VAR, $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); - } - # INDEL - if ($row[$ins] ne ".") { - my $skip = 0; - # Modify coordinte to conform to VCF? - my %inss = split(/[\|\:]/, $row[$ins]); - my @keys = sort { $inss{$b} <=> $inss{$a} } keys %inss; -# if ($inss{$keys[0]} > $row[$nvar]) { -# $nvarall = $inss{$keys[0]}; -# $VAR = $keys[0]; -# $row[$dp] += $nvarall; -# } - my $nins = $inss{$keys[0]}; - my $DP = $row[$dp]; - my $nREF = $DP - $nins; - #$skip++ if ($nins < $minVarDp); - #$skip++ if ($DP < $minDp); - my $vaf = $nins / $row[$dp]; - #$skip++ if ($vaf < $minVaf); - my $gt = "$row[$ref]/$keys[0]"; - my $qual = $row[$insQual]; - $skip++ if ($qual == 0); - my $filter = 0; - my $info = "TARGET=$row[$target]"; - my $format = "DP:AD:AB"; - my $sample = "$DP:$nREF,$nins:$vaf"; - print join("\t", @row[$chr, $pos], ".", $REF, $keys[0], $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); - } - if ($row[$del] ne ".") { - my $skip = 0; - # Modify coordinte to conform to VCF? - my %dels = split(/[\|\:]/, $row[$del]); - my @keys = sort { $dels{$b} <=> $dels{$a} } keys %dels; -# if ($dels{$keys[0]} > $row[$nvar]) { -# $nvarall = $dels{$keys[0]}; -# $REF = $keys[0]; -# $row[$dp] += $nvarall; -# } - my $ndel = $dels{$keys[0]}; - my $DP = $row[$dp]; - my $nREF = $DP - $ndel; - #$skip++ if ($ndel < $minVarDp); - #$skip++ if ($DP < $minDp); - my $vaf = $ndel / $DP; - #$skip++ if ($vaf < $minVaf); - my $gt = "$keys[0]/$row[$ref]"; - my $qual = $row[$delQual]; - $skip++ if ($qual == 0); - my $filter = 0; - my $info = "TARGET=$row[$target]"; - my $format = "DP:AD:AB"; - my $sample = "$DP:$nREF,$ndel:$vaf"; - print join("\t", @row[$chr, $pos], ".", $keys[0], $row[$ref], $qual, $filter, $info, $format, $sample) . "\n" if ($skip == 0); - } -} -close QC; -
--- a/falco/misc/qcFilt.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -#!/usr/bin/perl - -use strict; - -my $qcQual = shift; -my $clinvar = shift; -my $cosmic = shift; -my $cosmicNC = shift; -my $output = shift; - -my $minDp = shift || 100; -my $minVar = shift || 10; -my $minIns = shift || $minVar; -my $minDel = shift || $minVar; -my $minVarQ = shift || 100; -my $minInsQ = shift || 200; -my $minDelQ = shift || 200; - -my %cvHsh = (); -print STDERR "Reading clinvars...\n"; -open CV, "<$clinvar"; -while (<CV>) { last if (/#CHROM/); } -while (<CV>) { - chomp; - my @row = split(/\t/, $_); - $cvHsh{"chr".$row[0].":".$row[1]} = [@row]; -} -close CV; - -print STDERR "Reading COSMIC...\n"; -open CV, "<$cosmic"; -while (<CV>) { last if (/#CHROM/); } -while (<CV>) { - chomp; - my @row = split(/\t/, $_); - $cvHsh{"chr".$row[0].":".$row[1]} = [@row]; -} -close CV; - -print STDERR "Reading COSMICNC...\n"; -open CV, "<$cosmicNC"; -while (<CV>) { last if (/#CHROM/); } -while (<CV>) { - chomp; - my @row = split(/\t/, $_); - $cvHsh{"chr".$row[0].":".$row[1]} = [@row]; -} - -close CV; -print STDERR "done!"; - -open QC, "<$qcQual"; -my $head = readline QC; -chomp; -$head =~ s/\s+$//; -my @rhead = split(/\t/, $head); -my $coln = 0; -my %col = map { $_ => $coln++ } @rhead; -open OUT, ">$output.qc.ann.qual.filt.txt"; -open CVOUT, ">$output.qc.ann.qual.clinvar.txt"; -print OUT "$head\n"; -print CVOUT "$head\n"; - -while (<QC>) { - my $line = $_; - my @row = split(/\t/, $_); - my $key = $row[$col{"X.chr"}] . ":" . $row[$col{pos}]; - if (exists($cvHsh{$key})) { - print CVOUT $line; - } - next if ($row[$col{dp}] < $minDp); - # Var - if ($row[$col{qScore}] >= $minVarQ && $row[$col{nVar}] > $minVar) { - print OUT $line; - } - # Ins - if ($row[$col{qScoreI}] >= $minInsQ) { - $row[$col{ins}] =~ /:(\d+)/; - if ($1 >= $minIns) { - print OUT $line; - } - } - # Del - if ($row[$col{qScoreD}] >= $minDelQ) { - $row[$col{del}] =~ /:(\d+)/; - if ($1 >= $minDel) { - print OUT $line; - } - } -} - -close OUT; -close CVOUT;
--- a/falco/misc/report.sh Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -base=$1 - -vcf2tsv=$DIR/../../misc/vcf2tsv.pl -spliteff=$DIR/splitEff.pl -addQc=$DIR/addQc.pl -filter=$DIR/filter.pl - -# convert to tsv -$vcf2tsv $base.samtools.vcf > $base.samtools.tsv -$vcf2tsv $base.vs.snp.a.vcf > $base.vs.snp.a.tsv - -# split eff columns -$spliteff $base.samtools.tsv > $base.res.tmp -$spliteff $base.vs.snp.a.tsv >> $base.res.tmp - -# add count data -$addQc $base.res.tmp $base.qc.ann.txt > $base.res.tsv - -# Filter -$filter $base.res.tsv > $base.res.filtered.tsv
--- a/falco/misc/splitEff.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -#!/usr/bin/perl -w -# -use strict; -my $file = shift; -my $tag = shift || "NoTag"; - -open F, "<$file"; -my $head = undef; -my %effIdx = (); -$effIdx{context} = 0; -while (<F>) { - if (/.*ID=EFF.*(\(.*\)).*/) { - my $str = $1; -# print STDERR $str . "\n"; - $str =~ s/\[.*\]//g; -# print STDERR $str . "\n"; - $str =~ s/^\(\s*(.*?)\s*\)$/$1/; -# print STDERR $str . "\n"; - my $c = 1; - $effIdx{lc($_)} = $c++ foreach split(/\s*\|\s*/, $str); -# print STDERR join("\n", map { $_ . ":" . $effIdx{$_} } keys(%effIdx)) . "\n"; -# exit; - } - if (/#CHROM/) { - $head = $_; - last; - } - -} - -chomp $head; -my @hrow = split(/\t/, $head); -my $colN = 0; -#my %col = map { print STDERR "$_ => $colN\n";$_ => $colN++ } @hrow; -my %col = map { $_ => $colN++ } @hrow; -# Add AD column -# Convert DP4 for samtools file -my $ADName = (grep { /\_AD/ } keys(%col))[0]; -if (exists($col{DP4})) { - $ADName = "DP4"; -} -my $ADCol = $col{$ADName}; - -my $DPName = (grep { /\_DP/ } keys(%col))[0]; -if (exists($col{DP})) { - $DPName = "DP"; -} -my $DPCol = $col{$DPName}; - -#print STDERR $ADName . "\t" . $col{$ADName} . " $ADCol\n"; - -#Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] ) -my @Col = qw/DP AD Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name Transcript_BioType Gene_Coding Transcript_ID Exon_Rank Tag/; - -my @effCol = map {lc} qw/Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name transcript_BioType Gene_Coding Transcript_ID Exon_Rank/; -my @effColOrd = map {$effIdx{$_}} @effCol; - -print join("\t", @hrow[0 ..5], @Col) . "\n"; #map { "eff$_" } 1 .. 10) . "\n"; -while (<F>) { - chomp; - my @row = split(/\t/, $_); - - if ($ADName eq "DP4") { - my @dp4row = split(/,/, $row[$ADCol]); -# print STDERR join(":", @dp4row) . "\n"; sleep 1; - $row[$ADCol] = ($dp4row[0] + $dp4row[1]) . "," . ($dp4row[2] + $dp4row[3]); - } - -# print $row[$col{EFF}] . "\n"; - my @effs = split(/,/, $row[$col{EFF}]); - foreach my $eff (@effs) { - $eff =~ s/\)$//; - my @effrow = split(/[\|\(\)]/, $eff, -1); - -# print STDERR scalar(@effrow) . " $eff\n"; -# print STDERR join(":", @effrow) . " $eff\n"; sleep 1; - print join("\t", @row[0 .. 5, $DPCol, $ADCol], @effrow[@effColOrd], $tag) . "\n"; - - } -} - -close F;
--- a/falco/misc/startAnalysis.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -#!/usr/bin/perl -w - -use strict; -use Sys::Hostname; - -my $dir = shift || undef; -my $tMax = shift || 2; -my $binDir = "/ccagc/lib/pipelines/TSACP/falco/"; -#my $binDir = "/ccagc/lib/daoud/AAP/amplicon-analysis-pipeline/"; -my @files = (); -my %pairs = (); -#if ($#ARGV == -1) { - -unless (-d $dir) { - &stderr($dir . " not found"); - exit; -} - -if ($dir) { - chdir $dir; - open FILES, "find -L ./ -iname \"*fastq.gz\"|"; - while (<FILES>) { - chomp; - push @files, $_; - } -} -else { - while (<STDIN>) { - chomp; - push @files, $_; - } -} - -if ($#files == -1) { - &stderr("No fastq found, exiting"); - exit; -} - -foreach my $f (@files) { - chomp $f; - $f =~ /^(.*)\/(.*)_(.*?)_(.*?)_(.*?)_(.*?)$/; - next if ($3 =~ /Undetermined/); - #print $2 . " $f\n"; - $pairs{$2}{$5} = $f; - -} -my $bin = "$binDir/amplicon-Al-TSACP.sh"; -my $dstamp = `date +"%y%m%d"`; -my $tCnt = 0; -my %pidHsh = (); -#print STDERR "PID $$\n"; -&stderr("PID $$"); -foreach my $pair (keys(%pairs)) { - next if ($pair =~ /Undetermined/); - my $pid = fork; - print "$$ $pid \n"; - sleep 1; - if ($pid) { - $pidHsh{$pid} = localtime(); -# print STDERR localtime() . " : Forking $pid : $pair\n"; - &stderr("Forking $pid : $pair"); - while (scalar(keys(%pidHsh)) >= $tMax) { - my $deceased = wait; - #print STDERR localtime() . " : $deceased $pidHsh{$deceased} finished\n" if (exists($pidHsh{$deceased})); - &stderr("$deceased $pidHsh{$deceased} finished") if (exists($pidHsh{$deceased})); - delete($pidHsh{$deceased}); - } - sleep 1; - } - else { -# print STDERR localtime() . " : Child $$ forked??\n"; - &stderr("Child $$ forked"); - system("$bin $pairs{$pair}{R1} $pairs{$pair}{R2} $pair > $pair.log 2>&1"); - &stderr("Child $$ done"); - exit; - #print STDERR localtime() . " : Child $$ I should be dead by now,...\n"; - } -} - -1 while (wait() != -1); - -my $bin2 = "$binDir/amplicon-QC.sh"; -#print STDERR localtime() . " : Generating run QC $bin2\n"; -&stderr("Generating run QC $bin2"); -system($bin2); -my $bin3 = "$binDir/misc/mkHtmlReport.pl ./ ./"; -#print STDERR localtime() . " : Generating HTML $bin3\n"; -&stderr("Generating HTML $bin3"); -system($bin3); - -sub stderr { - my $msg = shift; - print STDERR localtime() . " [" . hostname . "] [$$] : $msg\n"; -}
--- a/falco/misc/varFilter.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -#!/usr/bin/perl -# -# Take target regions and call variants based on simple depth en frequency thresholds - -my $minDepth = shift || 100; -my $minFreq = shift || 0.01; -my $minVar = shift || 10; - -my $depthCol = 3; -my $varCol = 7; -my %nt = ( - A => 8, - C => 9, - G => 10, - T => 11, -); -my $input = shift; -my $fh = undef; -if (defined $input) { - open ($fh, "<$input"); -} -else { - $fh = *STDIN unless (defined $fh); -} - -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Mutant25 -my $prevNT = ""; -print "##fileformat=VCFv4.1\n"; -print "##INFO=<ID=TARGET,Number=1,Type=String,Description=\"Target description\">\n"; -print "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n"; -print "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n"; -print "##FORMAT=<ID=AD,Number=2,Type=Integer,Description=\"Allele Distribution\">\n"; -print "##FORMAT=<ID=VAF,Number=1,Type=Float,Description=\"Variant Allele Frequency\">\n"; -print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\n"; - -while (<$fh>) { - chomp; - my @row = split(/\t/, $_); - - my %var = map { $_ , $row[$nt{$_}] } split(/\//, $row[5]); - my $varNT = (sort { $var{$b} <=> $var{$a} } keys(%var))[0]; - - my $depth = $row[$depthCol]; - my $freq = $var{$varNT} / $depth; - if (($row[2] ne ".") && ($minDepth <= $depth)) { - my $qual = 100; - my $filt = "."; - $row[2] =~ s/\|/,/g; - my $info = "TARGET:$row[2];DP:$depth"; - - if ($row[13] ne ".") { - my %ins = split(/[\|:]/, $row[13]); - my $maxIns = (sort {$ins{$b} <=> $ins{$a}} keys(%ins))[0]; - my $iFreq = $ins{$maxIns}; - my $VAF = $iFreq / ($iFreq + $row[6]); - $maxIns =~ s/^\+//; - if ($VAF > $minFreq && $minVar <= $iFreq) { - my $format = "DP:AD:VAF\tDP=$depth:AD=$row[6],$iFreq:VAF=$VAF"; - print join("\t", @row[0 .. 1], ".", $prevNT . $row[4], $prevNT . $row[4] . $maxIns, $qual, $filt, $info, $format) . "\n"; - } - } - - if ($row[14] ne ".") { - my %del = split(/[\|:]/, $row[14]); - my $maxDel = (sort {$del{$b} <=> $del{$a}} keys(%del))[0]; - my $dFreq = $del{$maxDel}; - my $VAF = $dFreq / ($dFreq + $row[6]); - $maxDel =~ s/^-//; - if ($VAF > $minFreq && $minVar <= $dFreq) { - my $format = "DP:AD:VAF\tDP=$depth:AD=$row[6],$dFreq:VAF=$VAF"; - print join("\t", @row[0 .. 1], ".", $prevNT . $maxDel, $prevNT, $qual, $filt, $info, $format) . "\n"; - } - } - - - if ($minFreq <= $freq && $minVar <= $var{$varNT}) { - my $format = "DP:AD:VAF\tDP=$depth:AD=$row[6],$var{$varNT}:VAF=$freq"; - my $varNT = substr($row[5], 0, 1); - print join("\t", @row[0 .. 1], ".", $row[4], $varNT, $qual, $filt, $info, $format) . "\n"; - } - } - $prevNT = $row[4]; -}
--- a/falco/misc/vcf2tsv.pl Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -#!/usr/bin/perl -w - -use strict; - -my @vcfs = @ARGV; - -my @info = (); -my @format = (); -my $header = ""; - -foreach my $vcf (0 .. $#vcfs) { - open V, "<$vcfs[$vcf]"; - while (<V>) { - if (/^#CHROM/) { - if ($vcf == 0) { - chomp; - my @row = split(/\t/, $_); - print $header; - print join("\t", @row[0 .. 6], @info) . "\t"; - my @sampleRow = (); - foreach my $s (9 .. $#row) { -# print join("\t", map { "S$s" . "_$_" } @format) . "\n"; - push @sampleRow, map { $row[$s] . "_$_" } @format; - } - print join("\t", @sampleRow) . "\n"; - } - last; - } - if (/^##INFO/ && ($vcf == 0)) { - /ID=(.*?),/; - push @info, $1; - } - elsif (/^##FORMAT/ && ($vcf == 0)) { - /ID=(.*?),/; - push @format, $1; - } - $header .= $_; - } - - while (<V>) { - print join("\t", @{ &readTags(\$_) }) . "\n"; - } - close V; -} - -sub readTags { - my $line = shift; - chomp $$line; - my @row = split(/\t/, $$line); - my @res = (@row[0 .. 6]); - my @infoDat = split(/[;]/, $row[7]); - my @formatDat1 = split(/:/, $row[8]); - my %infoHsh = (); - foreach my $i (@infoDat) { - my @e = split(/=/, $i); - $infoHsh{$e[0]} = defined($e[1])?$e[1]:"1"; - } - - foreach my $t (0 .. $#info) { - push @res, defined($infoHsh{$info[$t]})?$infoHsh{$info[$t]}:"."; - } - - foreach my $s (9 .. $#row) { - my %formatHsh = (); - my @formatDat2 = split(/:/, $row[$s]); - $formatHsh{$formatDat1[$_]} = $formatDat2[$_] foreach (0 .. $#formatDat1); - - foreach my $i (0 .. $#format) { - push @res, defined($formatHsh{$format[$i]})?$formatHsh{$format[$i]}:"."; - } - } - return \@res; -}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/TSACP/TSACP.bed Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,221 @@ +chr1 43814981 43815163 MPL1_2.chr1.43815008.43815009_tile_1 100 + 43815005 43815137 +chr1 115256499 115256680 NRAS1_7.chr1.115256528.115256531_tile_1 100 + 115256525 115256653 +chr1 115258701 115258884 NRAS8_13.chr1.115258730.115258748_tile_1 100 + 115258727 115258855 +chr2 29432635 29432822 ALK1.chr2.29432664.29432664_tile_1 100 + 29432662 29432795 +chr2 29443666 29443836 ALK2.chr2.29443695.29443695_tile_1 100 + 29443691 29443810 +chr2 209113083 209113264 IDH1_1_2.chr2.209113112.209113113_tile_1 100 + 209113110 209113237 +chr2 212288911 212289100 ERBB4_1_2.chr2.212288942.212288955_tile_1 100 + 212288938 212289073 +chr2 212530035 212530210 ERBB4_3_4.chr2.212530066.212530135_tile_1 100 + 212530061 212530183 +chr2 212576820 212576990 ERBB4_5.chr2.212576857.212576857_tile_1 100 + 212576850 212576960 +chr2 212578314 212578499 ERBB4_6_7.chr2.212578341.212578349_tile_1 100 + 212578339 212578470 +chr2 212587114 212587285 ERBB4_8.chr2.212587147.212587147_tile_1 100 + 212587141 212587258 +chr2 212589782 212589957 ERBB4_9.chr2.212589811.212589811_tile_1 100 + 212589809 212589930 +chr2 212652705 212652876 ERBB4_10.chr2.212652764.212652764_tile_1 100 + 212652735 212652849 +chr2 212812126 212812311 ERBB4_11.chr2.212812157.212812157_tile_1 100 + 212812155 212812284 +chr3 10183768 10183952 VHL1_2.chr3.10183797.10183817_tile_1 100 + 10183793 10183926 +chr3 10188216 10188401 VHL3_5.chr3.10188245.10188301_tile_1 100 + 10188243 10188374 +chr3 10191449 10191634 VHL6_8.chr3.10191480.10191506_tile_1 100 + 10191477 10191607 +chr3 37067211 37067394 MLH1.chr3.37067240.37067240_tile_1 100 + 37067237 37067367 +chr3 41266009 41266180 CTNNB1_1_16.chr3.41266040.41266137_tile_1 100 + 41266036 41266153 +chr3 178916835 178917024 PIK3CA1.chr3.178916876.178916876_tile_1 100 + 178916861 178916997 +chr3 178921524 178921709 PIK3CA2.chr3.178921553.178921553_tile_1 100 + 178921551 178921682 +chr3 178927905 178928082 PIK3CA3.chr3.178927980.178927980_tile_1 100 + 178927932 178928055 +chr3 178936043 178936214 PIK3CA4_11.chr3.178936074.178936095_tile_1 100 + 178936070 178936187 +chr3 178938831 178939004 PIK3CA12.chr3.178938860.178938860_tile_1 100 + 178938858 178938977 +chr3 178951880 178952054 PIK3CA13_20.chr3.178952007.178952150_tile_1 100 + 178951906 178952026 +chr3 178951998 178952184 PIK3CA13_20.chr3.178952007.178952150_tile_2 100 - 178952025 178952154 +chr4 1803537 1803712 FGFR3_1_2.chr4.1803564.1803568_tile_1 100 + 1803562 1803685 +chr4 1806090 1806277 FGFR3_3_4.chr4.1806119.1806153_tile_1 100 + 1806117 1806250 +chr4 1807835 1808025 FGFR3_5_7.chr4.1807862.1807890_tile_1 100 + 1807857 1807999 +chr4 1808294 1808464 FGFR3_8.chr4.1808331.1808331_tile_1 100 + 1808316 1808442 +chr4 1808920 1809105 FGFR3_9.chr4.1808949.1808949_tile_1 100 + 1808943 1809078 +chr4 55140980 55141157 PDGFRA1_4.chr4.55141013.55141049_tile_1 100 + 55141007 55141130 +chr4 55144119 55144306 PDGFRA5.chr4.55144146.55144146_tile_1 100 + 55144145 55144279 +chr4 55144518 55144703 PDGFRA6.chr4.55144547.55144547_tile_1 100 + 55144544 55144676 +chr4 55152011 55152184 PDGFRA7_23.chr4.55152040.55152109_tile_1 100 + 55152036 55152157 +chr4 55561735 55561913 KIT1.chr4.55561764.55561764_tile_1 100 + 55561762 55561887 +chr4 55592154 55592341 KIT2.chr4.55592185.55592186_tile_1 100 + 55592180 55592314 +chr4 55593341 55593512 KIT3_19.chr4.55593464.55593689_tile_1 100 + 55593365 55593483 +chr4 55593435 55593609 KIT3_19.chr4.55593464.55593689_tile_2 100 - 55593461 55593583 +chr4 55593555 55593739 KIT3_19.chr4.55593464.55593689_tile_3 100 + 55593582 55593713 +chr4 55594192 55594380 KIT20_21.chr4.55594221.55594258_tile_1 100 + 55594219 55594352 +chr4 55595492 55595675 KIT22.chr4.55595519.55595519_tile_1 100 + 55595518 55595646 +chr4 55597466 55597652 KIT23.chr4.55597495.55597497_tile_1 100 + 55597493 55597624 +chr4 55599289 55599472 KIT24_28.chr4.55599320.55599348_tile_1 100 + 55599316 55599445 +chr4 55602665 55602850 KIT29.chr4.55602694.55602694_tile_1 100 + 55602690 55602823 +chr4 55945983 55946155 KDR1.chr4.55946114.55946257_tile_1 100 + 55946013 55946125 +chr4 55946097 55946284 KDR1.chr4.55946114.55946257_tile_2 100 - 55946124 55946257 +chr4 55953776 55953965 KDR3.chr4.55953807.55953807_tile_1 100 + 55953803 55953938 +chr4 55955084 55955257 KDR4.chr4.55955111.55955127_tile_1 100 + 55955108 55955230 +chr4 55960958 55961129 KDR6.chr4.55960989.55961023_tile_1 100 + 55960985 55961102 +chr4 55962476 55962653 KDR8.chr4.55962507.55962507_tile_1 100 + 55962502 55962626 +chr4 55972935 55973106 KDR9.chr4.55972964.55972964_tile_1 100 + 55972962 55973079 +chr4 55979594 55979775 KDR10.chr4.55979623.55979623_tile_1 100 + 55979620 55979748 +chr4 55980319 55980496 KDR11.chr4.55980348.55980348_tile_1 100 + 55980346 55980469 +chr4 153245415 153245604 FBXW7_1.chr4.153245446.153245446_tile_1 100 + 153245442 153245575 +chr4 153247247 153247417 FBXW7_2.chr4.153247288.153247366_tile_1 100 + 153247277 153247389 +chr4 153249337 153249520 FBXW7_5.chr4.153249384.153249384_tile_1 100 + 153249364 153249493 +chr4 153250852 153251031 FBXW7_7.chr4.153250883.153250883_tile_1 100 + 153250878 153251004 +chr4 153258952 153259142 FBXW7_8.chr4.153258983.153258983_tile_1 100 + 153258980 153259112 +chr5 112173886 112174071 APC1.chr5.112173917.112173917_tile_1 100 + 112173913 112174044 +chr5 112174602 112174775 APC2.chr5.112174631.112174631_tile_1 100 + 112174629 112174748 +chr5 112175033 112175208 APC3_42.chr5.112175162.112175958_tile_1 100 - 112175061 112175181 +chr5 112175127 112175297 APC3_42.chr5.112175162.112175958_tile_2 100 + 112175154 112175273 +chr5 112175215 112175386 APC3_42.chr5.112175162.112175958_tile_3 100 - 112175243 112175361 +chr5 112175305 112175475 APC3_42.chr5.112175162.112175958_tile_4 100 + 112175335 112175447 +chr5 112175393 112175566 APC3_42.chr5.112175162.112175958_tile_5 100 - 112175419 112175539 +chr5 112175511 112175683 APC3_42.chr5.112175162.112175958_tile_6 100 + 112175537 112175657 +chr5 112175629 112175799 APC3_42.chr5.112175162.112175958_tile_7 100 - 112175656 112175771 +chr5 112175739 112175911 APC3_42.chr5.112175162.112175958_tile_8 100 + 112175769 112175881 +chr5 112175853 112176042 APC3_42.chr5.112175162.112175958_tile_9 100 - 112175880 112176015 +chr5 149433615 149433799 CSF1R1_3.chr5.149433644.149433646_tile_1 100 + 149433642 149433773 +chr5 149453015 149453189 CSF1R4.chr5.149453044.149453044_tile_1 100 + 149453042 149453163 +chr5 170837492 170837677 NPM1.chr5.170837547.170837548_tile_1 100 + 170837518 170837650 +chr7 55211051 55211238 EGFR1.chr7.55211080.55211080_tile_1 100 + 55211078 55211211 +chr7 55221791 55221964 EGFR2.chr7.55221822.55221822_tile_1 100 + 55221817 55221937 +chr7 55233018 55233203 EGFR3.chr7.55233043.55233043_tile_1 100 + 55233041 55233176 +chr7 55241648 55241827 EGFR4.chr7.55241677.55241708_tile_1 100 + 55241674 55241800 +chr7 55242387 55242576 EGFR9.chr7.55242418.55242511_tile_1 100 + 55242415 55242549 +chr7 55248878 55249052 EGFR44.chr7.55249005.55249131_tile_1 100 + 55248904 55249026 +chr7 55249002 55249178 EGFR44.chr7.55249005.55249131_tile_2 100 - 55249025 55249152 +chr7 55259485 55259662 EGFR54.chr7.55259514.55259524_tile_1 100 + 55259512 55259635 +chr7 116339613 116339792 MET1.chr7.116339642.116339642_tile_1 100 + 116339640 116339765 +chr7 116340233 116340420 MET2.chr7.116340262.116340262_tile_1 100 + 116340260 116340393 +chr7 116411957 116412127 MET3.chr7.116411990.116411990_tile_1 100 + 116411983 116412099 +chr7 116417430 116417620 MET4.chr7.116417463.116417464_tile_1 100 + 116417457 116417592 +chr7 116423384 116423555 MET6.chr7.116423413.116423474_tile_1 100 + 116423410 116423528 +chr7 128845072 128845257 SMO1.chr7.128845101.128845101_tile_1 100 + 128845096 128845232 +chr7 128846009 128846194 SMO2.chr7.128846040.128846040_tile_1 100 + 128846036 128846167 +chr7 128846347 128846536 SMO3.chr7.128846374.128846374_tile_1 100 + 128846372 128846509 +chr7 128850310 128850499 SMO4.chr7.128850341.128850341_tile_1 100 + 128850334 128850472 +chr7 128851562 128851734 SMO5.chr7.128851593.128851593_tile_1 100 + 128851589 128851708 +chr7 140453092 140453267 BRAF1.chr7.140453121.140453193_tile_1 100 + 140453118 140453240 +chr7 140481368 140481545 BRAF28.chr7.140481397.140481478_tile_1 100 + 140481395 140481518 +chr8 38282182 38282360 FGFR1_1.chr8.38282209.38282209_tile_1 100 + 38282207 38282334 +chr8 38285907 38286090 FGFR1_2.chr8.38285938.38285938_tile_1 100 + 38285934 38286063 +chr9 5073736 5073923 JAK2_1.chr9.5073769.5073770_tile_1 100 + 5073764 5073894 +chr9 21971122 21971308 CDKN2A1.chr9.21971153.21971187_tile_1 100 + 21971147 21971282 +chr9 133738301 133738491 ABL1_1.chr9.133738330.133738364_tile_1 100 + 133738327 133738465 +chr9 133747475 133747664 ABL1_9.chr9.133747520.133747520_tile_1 100 + 133747502 133747641 +chr9 133748156 133748327 ABL1_10.chr9.133748283.133748414_tile_1 100 - 133748186 133748302 +chr9 133748276 133748457 ABL1_10.chr9.133748283.133748414_tile_2 100 + 133748301 133748434 +chr9 133750327 133750516 ABL1_16.chr9.133750356.133750356_tile_1 100 + 133750351 133750489 +chr9 139397739 139397928 NOTCH1_1.chr9.139397768.139397768_tile_1 100 + 139397765 139397901 +chr9 139399315 139399485 NOTCH1_2.chr9.139399344.139399422_tile_1 100 + 139399341 139399459 +chr10 43609047 43609226 RET1.chr10.43609078.43609104_tile_1 100 + 43609073 43609201 +chr10 43609901 43610075 RET2_9.chr10.43609940.43609950_tile_1 100 - 43609929 43610049 +chr10 43613809 43613998 RET10.chr10.43613840.43613840_tile_1 100 + 43613832 43613971 +chr10 43615532 43615703 RET11_12.chr10.43615567.43615569_tile_1 100 + 43615560 43615678 +chr10 43617387 43617564 RET13.chr10.43617416.43617416_tile_1 100 + 43617414 43617537 +chr10 89624213 89624388 PTEN1.chr10.89624242.89624244_tile_1 100 + 89624240 89624361 +chr10 89685274 89685459 PTEN3.chr10.89685307.89685307_tile_1 100 + 89685303 89685432 +chr10 89711864 89712039 PTEN4.chr10.89711893.89711900_tile_1 100 + 89711890 89712012 +chr10 89717488 89717668 PTEN7.chr10.89717615.89717772_tile_1 100 + 89717514 89717638 +chr10 89717614 89717801 PTEN7.chr10.89717615.89717772_tile_2 100 - 89717637 89717772 +chr10 89720683 89720870 PTEN13.chr10.89720716.89720852_tile_1 100 + 89720708 89720843 +chr10 89720813 89720991 PTEN13.chr10.89720716.89720852_tile_2 100 - 89720842 89720961 +chr10 123258005 123258184 FGFR2_1.chr10.123258034.123258034_tile_1 100 + 123258032 123258157 +chr10 123274745 123274930 FGFR2_2.chr10.123274774.123274803_tile_1 100 + 123274772 123274903 +chr10 123279384 123279555 FGFR2_5.chr10.123279503.123279677_tile_1 100 + 123279411 123279528 +chr10 123279470 123279640 FGFR2_5.chr10.123279503.123279677_tile_2 100 - 123279498 123279614 +chr10 123279586 123279769 FGFR2_5.chr10.123279503.123279677_tile_3 100 + 123279613 123279742 +chr11 533842 534021 HRAS1.chr11.533873.533875_tile_1 100 + 533868 533994 +chr11 534250 534434 HRAS6.chr11.534285.534289_tile_1 100 + 534277 534410 +chr11 108117816 108117989 ATM1.chr11.108117847.108117848_tile_1 100 + 108117845 108117962 +chr11 108119792 108119963 ATM2.chr11.108119823.108119823_tile_1 100 + 108119819 108119936 +chr11 108123512 108123683 ATM3.chr11.108123551.108123551_tile_1 100 + 108123541 108123654 +chr11 108137938 108138126 ATM4.chr11.108137973.108138003_tile_1 100 + 108137967 108138096 +chr11 108155103 108155281 ATM6.chr11.108155132.108155132_tile_1 100 + 108155130 108155251 +chr11 108170441 108170618 ATM7.chr11.108170476.108170479_tile_1 100 + 108170468 108170591 +chr11 108172390 108172571 ATM9.chr11.108172421.108172421_tile_1 100 + 108172417 108172544 +chr11 108173611 108173801 ATM10.chr11.108173640.108173640_tile_1 100 + 108173635 108173771 +chr11 108180914 108181101 ATM11.chr11.108180945.108180945_tile_1 100 + 108180942 108181074 +chr11 108200925 108201096 ATM12.chr11.108200958.108200961_tile_1 100 + 108200954 108201069 +chr11 108204650 108204823 ATM14.chr11.108204681.108204681_tile_1 100 + 108204679 108204796 +chr11 108205738 108205928 ATM15.chr11.108205769.108205769_tile_1 100 + 108205766 108205900 +chr11 108206565 108206750 ATM16.chr11.108206594.108206594_tile_1 100 + 108206592 108206723 +chr11 108218060 108218247 ATM17.chr11.108218089.108218089_tile_1 100 + 108218087 108218220 +chr11 108225561 108225751 ATM18.chr11.108225590.108225590_tile_1 100 + 108225588 108225725 +chr11 108236057 108236241 ATM19.chr11.108236086.108236203_tile_1 100 + 108236084 108236215 +chr12 25378531 25378717 KRAS1.chr12.25378562.25378562_tile_1 100 + 25378558 25378689 +chr12 25380244 25380427 KRAS2.chr12.25380275.25380283_tile_1 100 + 25380270 25380398 +chr12 25398224 25398414 KRAS7.chr12.25398255.25398285_tile_1 100 + 25398253 25398386 +chr12 112888134 112888323 PTPN11_1.chr12.112888163.112888211_tile_1 100 + 112888160 112888296 +chr12 112926855 112927032 PTPN11_10.chr12.112926884.112926888_tile_1 100 + 112926881 112927005 +chr12 121431384 121431558 HNF1A_1.chr12.121431413.121431414_tile_1 100 + 121431410 121431532 +chr12 121432041 121432221 HNF1A_3.chr12.121432070.121432070_tile_1 100 + 121432065 121432195 +chr13 28592589 28592766 FLT3_1.chr13.28592620.28592653_tile_1 100 + 28592617 28592739 +chr13 28602294 28602464 FLT3_13.chr13.28602329.28602329_tile_1 100 + 28602320 28602436 +chr13 28608213 28608402 FLT3_14.chr13.28608244.28608341_tile_1 100 + 28608242 28608375 +chr13 28610097 28610267 FLT3_22.chr13.28610138.28610138_tile_1 100 - 28610122 28610239 +chr13 48919155 48919336 RB1_1.chr13.48919244.48919244_tile_1 100 + 48919185 48919309 +chr13 48923119 48923296 RB1_2.chr13.48923148.48923148_tile_1 100 + 48923146 48923269 +chr13 48942654 48942826 RB1_3.chr13.48942685.48942685_tile_1 100 + 48942683 48942798 +chr13 48955503 48955684 RB1_4.chr13.48955538.48955550_tile_1 100 + 48955532 48955657 +chr13 49027111 49027288 RB1_6.chr13.49027168.49027168_tile_1 100 + 49027140 49027261 +chr13 49033812 49033989 RB1_7.chr13.49033843.49033846_tile_1 100 + 49033839 49033962 +chr13 49037814 49037985 RB1_8.chr13.49037877.49037877_tile_1 100 + 49037844 49037958 +chr13 49039131 49039304 RB1_9.chr13.49039164.49039164_tile_1 100 + 49039158 49039277 +chr14 105246428 105246600 AKT1.chr14.105246455.105246455_tile_1 100 + 105246452 105246574 +chr16 68835612 68835782 CDH1_1.chr16.68835649.68835650_tile_1 100 + 68835638 68835760 +chr16 68846108 68846283 CDH1_2.chr16.68846137.68846137_tile_1 100 + 68846135 68846256 +chr16 68847245 68847422 CDH1_3.chr16.68847274.68847277_tile_1 100 + 68847272 68847395 +chr17 7573976 7574147 TP53_1.chr17.7574003.7574021_tile_1 100 + 7574001 7574120 +chr17 7576995 7577166 TP53_3.chr17.7577022.7577129_tile_1 100 + 7577020 7577139 +chr17 7577494 7577683 TP53_17.chr17.7577523.7577574_tile_1 100 + 7577521 7577656 +chr17 7578063 7578234 TP53_31_59.chr17.7578190.7578536_tile_1 100 + 7578091 7578207 +chr17 7578155 7578325 TP53_31_59.chr17.7578190.7578536_tile_2 100 - 7578180 7578303 +chr17 7578245 7578415 TP53_31_59.chr17.7578190.7578536_tile_3 100 + 7578273 7578389 +chr17 7578345 7578515 TP53_31_59.chr17.7578190.7578536_tile_4 100 - 7578373 7578491 +chr17 7578467 7578645 TP53_31_59.chr17.7578190.7578536_tile_5 100 + 7578490 7578619 +chr17 7579323 7579507 TP53_60.chr17.7579358.7579403_tile_1 100 + 7579350 7579481 +chr17 7579851 7580032 TP53_64.chr17.7579882.7579882_tile_1 100 + 7579878 7580005 +chr17 37880190 37880361 ERBB2_1.chr17.37880219.37880261_tile_1 100 + 37880216 37880334 +chr17 37880962 37881151 ERBB2_4.chr17.37880993.37881012_tile_1 100 + 37880986 37881124 +chr17 37881297 37881482 ERBB2_13.chr17.37881332.37881440_tile_1 100 + 37881324 37881455 +chr18 48575130 48575301 SMAD4_1.chr18.48575169.48575170_tile_1 100 + 48575160 48575272 +chr18 48581167 48581346 SMAD4_2.chr18.48581198.48581198_tile_1 100 + 48581195 48581319 +chr18 48584527 48584714 SMAD4_3.chr18.48584560.48584560_tile_1 100 + 48584553 48584687 +chr18 48586233 48586416 SMAD4_4.chr18.48586262.48586262_tile_1 100 + 48586260 48586389 +chr18 48591795 48591982 SMAD4_5.chr18.48591826.48591919_tile_1 100 + 48591822 48591955 +chr18 48593376 48593547 SMAD4_11.chr18.48593405.48593405_tile_1 100 + 48593402 48593520 +chr18 48602997 48603168 SMAD4_12.chr18.48603032.48603094_tile_1 100 + 48603025 48603139 +chr18 48604637 48604808 SMAD4_15.chr18.48604668.48604754_tile_1 100 + 48604663 48604781 +chr19 1206992 1207169 STK11_1.chr19.1207021.1207092_tile_1 100 + 1207019 1207142 +chr19 1220458 1220638 STK11_4.chr19.1220487.1220502_tile_1 100 + 1220484 1220614 +chr19 1221231 1221407 STK11_8.chr19.1221264.1221319_tile_1 100 - 1221259 1221381 +chr19 1223034 1223221 STK11_12.chr19.1223059.1223125_tile_1 100 + 1223057 1223196 +chr19 17945665 17945840 JAK3_1.chr19.17945696.17945696_tile_1 100 + 17945690 17945813 +chr19 17947980 17948169 JAK3_2.chr19.17948009.17948009_tile_1 100 + 17948004 17948142 +chr20 36031733 36031923 SRC.chr20.36031762.36031762_tile_1 100 + 36031760 36031895 +chr20 57484389 57484560 GNAS1.chr20.57484420.57484421_tile_1 100 + 57484416 57484533 +chr22 24133938 24134126 SMARCB1_1.chr22.24133967.24133990_tile_1 100 + 24133964 24134100 +chr22 24143209 24143383 SMARCB1_3.chr22.24143240.24143240_tile_1 100 + 24143235 24143357 +chr22 24145551 24145726 SMARCB1_4.chr22.24145582.24145582_tile_1 100 + 24145577 24145699 +chr22 24176323 24176495 SMARCB1_5_6.chr22.24176352.24176357_tile_1 100 + 24176350 24176469 +chr19 3114823 3115004 GNA11_4.chr19.3114942.3115070_tile_1 100 - 3114845 3114981 +chr19 3114957 3115133 GNA11_4.chr19.3114942.3115070_tile_2 100 + 3114980 3115111 +chr19 3118801 3118989 GNA11_5.chr19.3118922.3119051_tile_1 100 - 3118825 3118963 +chr19 3119207 3119395 GNA11_6.chr19.3119204.3119357_tile_2 100 - 3119232 3119373 +chr19 3120864 3121035 GNA11_7.chr19.3120987.3121177_tile_1 100 + 3120887 3121008 +chr19 3120984 3121170 GNA11_7.chr19.3120987.3121177_tile_2 100 - 3121006 3121144 +chr19 3121120 3121304 GNA11_7.chr19.3120987.3121177_tile_3 100 + 3121143 3121280 +chr9 80412405 80412592 GNAQ_4.chr9.80412436.80412564_tile_1 100 + 80412432 80412565 +chr9 80409248 80409421 GNAQ_5.chr9.80409379.80409508_tile_1 100 + 80409278 80409392 +chr9 80409334 80409510 GNAQ_5.chr9.80409379.80409508_tile_2 100 - 80409364 80409486 +chr9 80409458 80409639 GNAQ_5.chr9.80409379.80409508_tile_3 100 + 80409485 80409612 +chr9 80343305 80343476 GNAQ_6.chr9.80343430.80343583_tile_1 100 + 80343330 80343447 +chr9 80343391 80343561 GNAQ_6.chr9.80343430.80343583_tile_2 100 - 80343417 80343531 +chr9 80343503 80343689 GNAQ_6.chr9.80343430.80343583_tile_3 100 + 80343530 80343659 +chr9 80336109 80336280 GNAQ_7.chr9.80336240.80336429_tile_1 100 + 80336139 80336255 +chr9 80336203 80336374 GNAQ_7.chr9.80336240.80336429_tile_2 100 - 80336228 80336347 +chr9 80336319 80336495 GNAQ_7.chr9.80336240.80336429_tile_3 100 + 80336346 80336467 +chr22 17052963 17053133 PIK3CA4_11.chr3.178936074.178936095_tile_1 100 + 17052990 17053106 +chr22 17055412 17055585 PIK3CA12.chr3.178938860.178938860_tile_1 100 + 17055439 17055558 +chr9 33675956 33676480 PTEN7.chr10.89717615.89717772_tile_1 100 - 33675986 33676451 +chr9 33675628 33675815 PTEN13.chr10.89720716.89720852_tile_1 100 - 33675655 33675790 +chr7 65970149 65970483 GNA11_6.chr19.3119204.3119357_tile_2 100 + 65970175 65970458 +chr7 65970284 65970719 GNA11_7.chr19.3120987.3121177_tile_1 100 - 65970311 65970696 +chr2 132181237 132181750 GNAQ_5.chr9.80409379.80409508_tile_1 100 + 132181267 132181721 +chr2 132181447 132181600 GNAQ_6.chr9.80343430.80343583_tile_1 100 + 132181474 132181571 +chr2 132181331 132181839 GNAQ_7.chr9.80336240.80336429_tile_2 100 - 132181356 132181815
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,445 @@ +[Header] +Customer Name "ILLUMINA, INC." +Product Type 15032433 +Date Manufactured +Lot +DesignStudio ID NA +Target Plexity 212 + +[Probes] +Target Region Name Target Region ID Target ID Species Build ID Chromosome Start Position End Position Submitted Target Region Strand ULSO Sequence ULSO Genomic Hits DLSO Sequence DLSO Genomic Hits Probe Strand Designer Design Score Expected Amplifed Region Size SNP Masking Labels +MPL1_2 MPL1_2.chr1.43815008.43815009 MPL1_2.chr1.43815008.43815009_tile_1 Homo sapiens hg19 chr1 43815008 43815009 - AAGTGGCGAAGCCGTAGGTGCGCACG 0 TCAGCAGCAGCAGGCCCAGGACGG 0 - ILLUMINA NA 183 TRUE +NRAS1_7 NRAS1_7.chr1.115256528.115256531 NRAS1_7.chr1.115256528.115256531_tile_1 Homo sapiens hg19 chr1 115256528 115256531 - CAATAGCATTGCATTCCCTGTGGTTTT 0 AGAGTACAGTGCCATGAGAGACCAAT 0 - ILLUMINA NA 182 TRUE +NRAS8_13 NRAS8_13.chr1.115258730.115258748 NRAS8_13.chr1.115258730.115258748_tile_1 Homo sapiens hg19 chr1 115258730 115258748 - GGGTTTTCATTTCCATTGATTATAGAAAG 0 CTGACAATCCAGCTAATCCAGAACCA 0 - ILLUMINA NA 184 TRUE +ALK1 ALK1.chr2.29432664.29432664 ALK1.chr2.29432664.29432664_tile_1 Homo sapiens hg19 chr2 29432664 29432664 - GATAAAATCCTAGTGATGGCCGTTGTA 0 GACATCTACAGGTGAGTAAAGACTGCC 0 - ILLUMINA NA 188 TRUE +ALK2 ALK2.chr2.29443695.29443695 ALK2.chr2.29443695.29443695_tile_1 Homo sapiens hg19 chr2 29443695 29443695 - TGCTGCCCATGTTTACAGAATGCCTT 0 CACCAGAACATTGTTCGCTGCATTG 0 - ILLUMINA NA 171 TRUE +IDH1_1_2 IDH1_1_2.chr2.209113112.209113113 IDH1_1_2.chr2.209113112.209113113_tile_1 Homo sapiens hg19 chr2 209113112 209113113 - GAGGGTTGAGGAGTTCAAGTTGAAACA 0 CATGCTTATGGGGATCAAGTAAGTCAT 0 - ILLUMINA NA 182 TRUE +ERBB4_1_2 ERBB4_1_2.chr2.212288942.212288955 ERBB4_1_2.chr2.212288942.212288955_tile_1 Homo sapiens hg19 chr2 212288942 212288955 - ACTACTGGTATAGTGCTGGTTTGTTCA 0 AGAACGTTTGCCTCAGCCTCCCATCTG 0 - ILLUMINA NA 190 TRUE +ERBB4_3_4 ERBB4_3_4.chr2.212530066.212530135 ERBB4_3_4.chr2.212530066.212530135_tile_1 Homo sapiens hg19 chr2 212530066 212530135 - CATTTCAGGGTCCTGACAACTGTACAA 0 AACTGCACCCAAGGGTAAGCATTCTT 0 - ILLUMINA NA 176 TRUE +ERBB4_5 ERBB4_5.chr2.212576857.212576857 ERBB4_5.chr2.212576857.212576857_tile_1 Homo sapiens hg19 chr2 212576857 212576857 - ATACTCTGCTATTTTATAATGAAGATGCAA 0 CCAGTAACATTGACAAATTCATAAACTGTA 0 - ILLUMINA NA 171 TRUE +ERBB4_6_7 ERBB4_6_7.chr2.212578341.212578349 ERBB4_6_7.chr2.212578341.212578349_tile_1 Homo sapiens hg19 chr2 212578341 212578349 - AGGGTAAGATACATAAACACTATCAATGA 0 TGCCTGCCCTAGTTCCAAGATGGAA 0 - ILLUMINA NA 186 TRUE +ERBB4_8 ERBB4_8.chr2.212587147.212587147 ERBB4_8.chr2.212587147.212587147_tile_1 Homo sapiens hg19 chr2 212587147 212587147 - TGAAAGTAATATTTGCTGTGTTGCAGG 0 CATTCTGTGTCAAGAAATGTCCACGTA 0 - ILLUMINA NA 172 TRUE +ERBB4_9 ERBB4_9.chr2.212589811.212589811 ERBB4_9.chr2.212589811.212589811_tile_1 Homo sapiens hg19 chr2 212589811 212589811 - GCAGACTTTGATCATGGTCCTATCTCT 0 GACTGCTTTGTATGTCTGTGATTTCTC 0 - ILLUMINA NA 176 TRUE +ERBB4_10 ERBB4_10.chr2.212652764.212652764 ERBB4_10.chr2.212652764.212652764_tile_1 Homo sapiens hg19 chr2 212652764 212652764 - AATGGTGGAGTCTATGTAGACCAGAAC 0 TCTTTTTAATTTCTCAAAATGTTCTACCCT 0 - ILLUMINA NA 172 TRUE +ERBB4_11 ERBB4_11.chr2.212812157.212812157 ERBB4_11.chr2.212812157.212812157_tile_1 Homo sapiens hg19 chr2 212812157 212812157 - GTGGCTCTTAATCAGTTTCGTTACCTG 0 GGTAAGGAATATATCCAAAATGGCAAATA 0 - ILLUMINA NA 186 TRUE +VHL1_2 VHL1_2.chr3.10183797.10183817 VHL1_2.chr3.10183797.10183817_tile_1 Homo sapiens hg19 chr3 10183797 10183817 - AAAATGGACCCCGGGGCGGTAGAGGG 0 ATACGGGCAGCACGACGCGCGGACT 0 - ILLUMINA NA 185 TRUE +VHL3_5 VHL3_5.chr3.10188245.10188301 VHL3_5.chr3.10188245.10188301_tile_1 Homo sapiens hg19 chr3 10188245 10188301 - GAACTGGGCTTAATTTTTCAAGTGGTC 0 AGAAGCCCATCGTGTGTCCCTGCATCT 0 - ILLUMINA NA 186 TRUE +VHL6_8 VHL6_8.chr3.10191480.10191506 VHL6_8.chr3.10191480.10191506_tile_1 Homo sapiens hg19 chr3 10191480 10191506 - TTGATGTGCAATGCGCTCCTGTGTCAG 0 GTATACACTGGAAGGGCAAAAACCAAAT 0 - ILLUMINA NA 186 TRUE +MLH1 MLH1.chr3.37067240.37067240 MLH1.chr3.37067240.37067240_tile_1 Homo sapiens hg19 chr3 37067240 37067240 - TGGGAGTTCAAGCATCTCCTCATCTTG 0 ATCTGGTGGGCATAGACCTTATCACT 0 - ILLUMINA NA 184 TRUE +CTNNB1_1_16 CTNNB1_1_16.chr3.41266040.41266137 CTNNB1_1_16.chr3.41266040.41266137_tile_1 Homo sapiens hg19 chr3 41266040 41266137 - GGTATCCACATCCTCTTCCTCAGGATT 0 GTCCAACTCCATCAAATCAGCTATAAA 0 - ILLUMINA NA 172 TRUE +PIK3CA1 PIK3CA1.chr3.178916876.178916876 PIK3CA1.chr3.178916876.178916876_tile_1 Homo sapiens hg19 chr3 178916876 178916876 - AGGGACAACAGTTAAGCTTTATGGTTA 0 AAAAATTCTTCCCTTTCTGCTTCTTG 0 - ILLUMINA NA 190 TRUE +PIK3CA2 PIK3CA2.chr3.178921553.178921553 PIK3CA2.chr3.178921553.178921553_tile_1 Homo sapiens hg19 chr3 178921553 178921553 - ACATTCGGAGATTTGGATGTTCTCCTA 0 TCACGTAGGTTGCACAAAGAATTTTTA 0 - ILLUMINA NA 186 TRUE +PIK3CA3 PIK3CA3.chr3.178927980.178927980 PIK3CA3.chr3.178927980.178927980_tile_1 Homo sapiens hg19 chr3 178927980 178927980 - CTTCTAATCCATGAGGTACTGGCCAAA 0 AACACATTTCAAAACACTTTTCTTCCC 0 - ILLUMINA NA 178 TRUE +PIK3CA4_11 PIK3CA4_11.chr3.178936074.178936095 PIK3CA4_11.chr3.178936074.178936095_tile_1 Homo sapiens hg19 chr3 178936074 178936095 - GGTATGGTAAAAACATGCTGAGATCAG 0 CTCGTGTAGAAATTGCTTTGAGCTGTT 0 - ILLUMINA NA 172 TRUE +PIK3CA12 PIK3CA12.chr3.178938860.178938860 PIK3CA12.chr3.178938860.178938860_tile_1 Homo sapiens hg19 chr3 178938860 178938860 - TAAACAACTCTGCCCCACTGCAGTGAA 0 CTTCAAATACATCCCACATGCACGACA 0 - ILLUMINA NA 174 TRUE +PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_1 Homo sapiens hg19 chr3 178952007 178952150 - CCAAAGCCTCTTGCTCAGTTTTATCTAA 0 AGCCTTGTAACACATCTCCTGAAACC 0 - ILLUMINA NA 175 TRUE +PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_2 Homo sapiens hg19 chr3 178952007 178952150 + CATTGCATACATTCGAAAGACCCTAGC 0 AGATAACTGAGAAAATGAAAGCTCACTCTG 0 + ILLUMINA NA 187 TRUE +FGFR3_1_2 FGFR3_1_2.chr4.1803564.1803568 FGFR3_1_2.chr4.1803564.1803568_tile_1 Homo sapiens hg19 chr4 1803564 1803568 - TTGCTGCCATTCACCTCCACGTGCTTG 0 TCTGTGGGGGCAGATGACGCTCAGG 0 - ILLUMINA NA 176 TRUE +FGFR3_3_4 FGFR3_3_4.chr4.1806119.1806153 FGFR3_3_4.chr4.1806119.1806153_tile_1 Homo sapiens hg19 chr4 1806119 1806153 - GCTCAGAACCTGGTATCTACTTTCTGT 0 TAGCTGAGGATGCCTGCATACACACTG 0 - ILLUMINA NA 188 TRUE +FGFR3_5_7 FGFR3_5_7.chr4.1807862.1807890 FGFR3_5_7.chr4.1807862.1807890_tile_1 Homo sapiens hg19 chr4 1807862 1807890 - AAACAAGGCCTCAGGCGCCATCCACT 0 GCCAGCCCGAAGTCTGCGATCT 0 - ILLUMINA NA 191 TRUE +FGFR3_8 FGFR3_8.chr4.1808331.1808331 FGFR3_8.chr4.1808331.1808331_tile_1 Homo sapiens hg19 chr4 1808331 1808331 - CCGGAGGGACCCCCACCCCTGA 0 CCCCCAGCGTGAAGATCTCCCA 0 - ILLUMINA NA 171 TRUE +FGFR3_9 FGFR3_9.chr4.1808949.1808949 FGFR3_9.chr4.1808949.1808949_tile_1 Homo sapiens hg19 chr4 1808949 1808949 - AAGCTCTGTGTAGCTGTCTCTCCATCT 0 TCGTGGGCAAACACGGAGTCGTC 0 - ILLUMINA NA 186 TRUE +PDGFRA1_4 PDGFRA1_4.chr4.55141013.55141049 PDGFRA1_4.chr4.55141013.55141049_tile_1 Homo sapiens hg19 chr4 55141013 55141049 - TACCCCATGGAACTTACCAAGCACTAG 0 CTATAAATGACCAGGACAGGTAACTGG 0 - ILLUMINA NA 178 TRUE +PDGFRA5 PDGFRA5.chr4.55144146.55144146 PDGFRA5.chr4.55144146.55144146_tile_1 Homo sapiens hg19 chr4 55144146 55144146 - GTCAGCTCCATTCAAGGGACTTCTATT 0 TACAATGTTCAAATGTGGCCCCAGGT 0 - ILLUMINA NA 188 TRUE +PDGFRA6 PDGFRA6.chr4.55144547.55144547 PDGFRA6.chr4.55144547.55144547_tile_1 Homo sapiens hg19 chr4 55144547 55144547 - AACATCTCTCTTTGCACCCACCTCCGT 0 ATGATGTAAATGGGGCCTATGGGGAC 0 - ILLUMINA NA 186 TRUE +PDGFRA7_23 PDGFRA7_23.chr4.55152040.55152109 PDGFRA7_23.chr4.55152040.55152109_tile_1 Homo sapiens hg19 chr4 55152040 55152109 - AGAGATTAAAGTGAAGGAGGATGAGCC 0 TTGCGAGCAGCCAGATCACGGTGGA 0 - ILLUMINA NA 174 TRUE +KIT1 KIT1.chr4.55561764.55561764 KIT1.chr4.55561764.55561764_tile_1 Homo sapiens hg19 chr4 55561764 55561764 - GTGTTTGTTGGTGCACGTGTATTTGC 0 CCCACGCGGACTATTAAGTCTGATTTT 0 - ILLUMINA NA 179 TRUE +KIT2 KIT2.chr4.55592185.55592186 KIT2.chr4.55592185.55592186_tile_1 Homo sapiens hg19 chr4 55592185 55592186 - CAGTATGGTGTGATGCATGTATTACCA 0 CAGAAGTCTTGCCCACATCGTTGTAA 0 - ILLUMINA NA 188 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_1 Homo sapiens hg19 chr4 55593464 55593689 - GAGAGAACAAATAAATGGTTACCTGTAAA 0 GTGGAATCACAAACTTTGGCAGGA 0 - ILLUMINA NA 172 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_2 Homo sapiens hg19 chr4 55593464 55593689 + CGTAGCTGGCATGATGTGCATTATTG 0 ACCCATGTATGAAGTACAGTGGAAGG 0 + ILLUMINA NA 175 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_3 Homo sapiens hg19 chr4 55593464 55593689 - GTGACATGGAAAGCCCCTGTTTCATA 0 TCTGTGGGGAGAAAGGGAAAAATAGAT 0 - ILLUMINA NA 185 TRUE +KIT20_21 KIT20_21.chr4.55594221.55594258 KIT20_21.chr4.55594221.55594258_tile_1 Homo sapiens hg19 chr4 55594221 55594258 - GCAGTTTATAATCTAGCATTGCCAAAAT 0 AGTTCAGACATGAGGGCTTCCCGTTCT 0 - ILLUMINA NA 189 TRUE +KIT22 KIT22.chr4.55595519.55595519 KIT22.chr4.55595519.55595519_tile_1 Homo sapiens hg19 chr4 55595519 55595519 - ACTATTTATGTAAATCAGTCTTACCAGGA 0 TAATGACCAGGGTGGGCCCTAAAAGC 0 - ILLUMINA NA 184 TRUE +KIT23 KIT23.chr4.55597495.55597497 KIT23.chr4.55597495.55597497_tile_1 Homo sapiens hg19 chr4 55597495 55597497 - CCACATTAGCATGATATACATACTCTCT 0 CTGGGAGAGATGAAACAAGTCATGACT 0 - ILLUMINA NA 187 TRUE +KIT24_28 KIT24_28.chr4.55599320.55599348 KIT24_28.chr4.55599320.55599348_tile_1 Homo sapiens hg19 chr4 55599320 55599348 - TGTGTGATATCCCTAGACAGGATTTAC 0 GGCTAGACCAAAATCACAAATCTTTGT 0 - ILLUMINA NA 184 TRUE +KIT29 KIT29.chr4.55602694.55602694 KIT29.chr4.55602694.55602694_tile_1 Homo sapiens hg19 chr4 55602694 55602694 - GAAGCAGGACACCAATGAAACTTCAAG 0 TGCCATCCACTTCACAGGTAGTCGA 0 - ILLUMINA NA 186 TRUE +KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_1 Homo sapiens hg19 chr4 55946114 55946257 - ATTCTCCAGCCTGACTCGGGGACCACACTG 0 CATTTGATTTTCATTTCGACAACAGAAAAA 0 - ILLUMINA NA 173 TRUE +KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_2 Homo sapiens hg19 chr4 55946114 55946257 + ATGCTTCCTTTTAAACAGGAGGAGAGC 0 GGACTGGTAGCCGCTTGTCTGGTTTGA 0 + ILLUMINA NA 188 TRUE +KDR3 KDR3.chr4.55953807.55953807 KDR3.chr4.55953807.55953807_tile_1 Homo sapiens hg19 chr4 55953807 55953807 - CTGAAGCCATAACAACAGTCTTCTGTG 0 ATTCCATTATGACAACACAGCAGGAAT 0 - ILLUMINA NA 190 TRUE +KDR4 KDR4.chr4.55955111.55955127 KDR4.chr4.55955111.55955127_tile_1 Homo sapiens hg19 chr4 55955111 55955127 - TCCTTATTTAGCATCTCACCTCGTCAG 0 AGCCCAGTCAGAGACCCACGTTTT 0 - ILLUMINA NA 174 TRUE +KDR6 KDR6.chr4.55960989.55961023 KDR6.chr4.55960989.55961023_tile_1 Homo sapiens hg19 chr4 55960989 55961023 - TTTATAGACCAAAGGGGCACGATTCCG 0 TGTAGAAGAAGAGGAAGGTACTGGCTA 0 - ILLUMINA NA 172 TRUE +KDR8 KDR8.chr4.55962507.55962507 KDR8.chr4.55962507.55962507_tile_1 Homo sapiens hg19 chr4 55962507 55962507 - GGAAATGCATGTGGTCTGTAAACTAGG 0 AACACACAGTGAGCATCGAGCTCTCA 0 - ILLUMINA NA 178 TRUE +KDR9 KDR9.chr4.55972964.55972964 KDR9.chr4.55972964.55972964_tile_1 Homo sapiens hg19 chr4 55972964 55972964 - TACCATGGTAGGCTGCGTTGGAAGTTA 0 GACAAACCCATACCCTTGTGAAGAATG 0 - ILLUMINA NA 172 TRUE +KDR10 KDR10.chr4.55979623.55979623 KDR10.chr4.55979623.55979623_tile_1 Homo sapiens hg19 chr4 55979623 55979623 - CTGGTGTCCCTGTTTTTAGCATTAAAT 0 ACCTAAAAACCCAGTCTGGGAGTGAG 0 - ILLUMINA NA 182 TRUE +KDR11 KDR11.chr4.55980348.55980348 KDR11.chr4.55980348.55980348_tile_1 Homo sapiens hg19 chr4 55980348 55980348 - TCTGTGCAAAGTTATAGGCTTATTTGC 0 AGAACTGAACTAAATGTGGGGATTGAC 0 - ILLUMINA NA 178 TRUE +FBXW7_1 FBXW7_1.chr4.153245446.153245446 FBXW7_1.chr4.153245446.153245446_tile_1 Homo sapiens hg19 chr4 153245446 153245446 - CAGTAATTGATAGGAAGAGTATCCATACT 0 AACAAGTGGAATGGAACTCAAAGACAA 0 - ILLUMINA NA 190 TRUE +FBXW7_2 FBXW7_2.chr4.153247288.153247366 FBXW7_2.chr4.153247288.153247366_tile_1 Homo sapiens hg19 chr4 153247288 153247366 - GTTTTGTTTTGTTTTTCTGTTTCTCCCT 0 TATGATGGCAGGAGGGTTGTTAGTGGAGCA 0 - ILLUMINA NA 171 TRUE +FBXW7_5 FBXW7_5.chr4.153249384.153249384 FBXW7_5.chr4.153249384.153249384_tile_1 Homo sapiens hg19 chr4 153249384 153249384 - CATACAGGTGGAGTATGGTCATCACAA 0 AAAAGGTAAGGGAAAATCTTGTCATGG 0 - ILLUMINA NA 184 TRUE +FBXW7_7 FBXW7_7.chr4.153250883.153250883 FBXW7_7.chr4.153250883.153250883_tile_1 Homo sapiens hg19 chr4 153250883 153250883 - CTGTTCCTGTTTATGCCTTCATTTTTC 0 AGTTAGTGGTTCTGATGACAACACTT 0 - ILLUMINA NA 180 TRUE +FBXW7_8 FBXW7_8.chr4.153258983.153258983 FBXW7_8.chr4.153258983.153258983_tile_1 Homo sapiens hg19 chr4 153258983 153258983 - CTGTAATTTGGGACATCTGTTAAAACAATA 0 GACTTCATTTCATTGCTCCCTAAAGAGG 0 - ILLUMINA NA 191 TRUE +APC1 APC1.chr5.112173917.112173917 APC1.chr5.112173917.112173917_tile_1 Homo sapiens hg19 chr5 112173917 112173917 - GCAGAGCTTCTTCTAAGTGCATTTCTC 0 TGAAGAAGTTCCTGGATTTTCTGTTGC 0 - ILLUMINA NA 186 TRUE +APC2 APC2.chr5.112174631.112174631 APC2.chr5.112174631.112174631_tile_1 Homo sapiens hg19 chr5 112174631 112174631 - AATTTGTTGGTCTCTCTTCTTCTTCAT 0 TTTGTTTCTGAACCATTGGCTCCCCGT 0 - ILLUMINA NA 174 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_1 Homo sapiens hg19 chr5 112175162 112175958 + CTTGCAAAGTTTCTTCTATTAACCAAGA 0 TTCTGCTAATACCCTGCAAATAGCAGA 0 + ILLUMINA NA 176 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_2 Homo sapiens hg19 chr5 112175162 112175958 - TGCTGGATTTGGTTCTAGGGTGCT 0 CCTATTTCATCTTCAGCTGATGACAAA 0 - ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_3 Homo sapiens hg19 chr5 112175162 112175958 + GAAAAGATTGGAACTAGGTCAGCTGAAG 0 AGCGAAATCTCCCTCCAAAAGTGGT 0 + ILLUMINA NA 172 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_4 Homo sapiens hg19 chr5 112175162 112175958 - CTATCAAGTGAACTGACAGAAGTACATC 0 CCTGGCTGATTCTGAAGATAAACTAGAACC 0 - ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_5 Homo sapiens hg19 chr5 112175162 112175958 + CACCCAAAAGTCCACCTGAACACTAT 0 ATTATAAGCCCCAGTGATCTTCCAGAT 0 + ILLUMINA NA 174 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_6 Homo sapiens hg19 chr5 112175162 112175958 - CTCTCTCTTTTCAGCAGTAGGTGCTT 0 CACTTACCATTCCACTGCATGGTTCA 0 - ILLUMINA NA 173 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_7 Homo sapiens hg19 chr5 112175162 112175958 + CAAACCAAGCGAGAAGTACCTAAAAAT 0 AAAGTACTCCAGATGGATTTTCTTGTTC 0 + ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_8 Homo sapiens hg19 chr5 112175162 112175958 - CTCTGATTCTGTTTCATTCCCATTGTCATT 0 GTGGCAAAATGTAATAAAGTATCAGCATCT 0 - ILLUMINA NA 173 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_9 Homo sapiens hg19 chr5 112175162 112175958 + ATTAAGAATAATGCCTCCAGTTCAGGA 0 AGAAGAATGTATTATTTCTGCCATGCC 0 + ILLUMINA NA 190 TRUE +CSF1R1_3 CSF1R1_3.chr5.149433644.149433646 CSF1R1_3.chr5.149433644.149433646_tile_1 Homo sapiens hg19 chr5 149433644 149433646 - TCCCACCCTCAGGACTATACCAATCT 0 AGTTCTGCTGAGGAGTTGACGACAGGG 0 - ILLUMINA NA 185 TRUE +CSF1R4 CSF1R4.chr5.149453044.149453044 CSF1R4.chr5.149453044.149453044_tile_1 Homo sapiens hg19 chr5 149453044 149453044 - TCTTGGGTGGTGGGGACTATGTACCT 0 AACTTGAGCTCTGAGCAGAACCTCATC 0 - ILLUMINA NA 175 TRUE +NPM1 NPM1.chr5.170837547.170837548 NPM1.chr5.170837547.170837548_tile_1 Homo sapiens hg19 chr5 170837547 170837548 - GGTAGGGAAAGTTCTCACTCTGCATTA 0 AAAAAGAAATGTGGTTAAGGAACCAC 0 - ILLUMINA NA 186 TRUE +EGFR1 EGFR1.chr7.55211080.55211080 EGFR1.chr7.55211080.55211080_tile_1 Homo sapiens hg19 chr7 55211080 55211080 - CATCGGAACTGCTGTCTGCATTTATGA 0 GATGATCTGCAGGTTTTCCAAAGGAAT 0 - ILLUMINA NA 188 TRUE +EGFR2 EGFR2.chr7.55221822.55221822 EGFR2.chr7.55221822.55221822_tile_1 Homo sapiens hg19 chr7 55221822 55221822 - AAGCAAGGCAAACACATCCACCCAAAG 0 AAAGCTGTATTTGCCCTCGGGGTTCA 0 - ILLUMINA NA 174 TRUE +EGFR3 EGFR3.chr7.55233043.55233043 EGFR3.chr7.55233043.55233043_tile_1 Homo sapiens hg19 chr7 55233043 55233043 - AACTTGGGAGACATTTTTGATCTCTGA 0 TGCCGGGCAGGTCTTGACGCAGT 0 - ILLUMINA NA 186 TRUE +EGFR4 EGFR4.chr7.55241677.55241708 EGFR4.chr7.55241677.55241708_tile_1 Homo sapiens hg19 chr7 55241677 55241708 - GGAAATATACAGCTTGCAAGGACTCTG 0 TCAAGATCCTCAAGAGAGCTTGGTTG 0 - ILLUMINA NA 180 TRUE +EGFR9 EGFR9.chr7.55242418.55242511 EGFR9.chr7.55242418.55242511_tile_1 Homo sapiens hg19 chr7 55242418 55242511 - ATGAGAAAAGGTGGGCCTGAGGTTCAG 0 CCTATGACAGAGAGAGAAGGAAGACGTT 0 - ILLUMINA NA 190 TRUE +EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_1 Homo sapiens hg19 chr7 55249005 55249131 - AGGTGAGGCAGATGCCCAGCAGGCGG 0 CGCATGAATGCGATCTTGAGTTTCAA 0 - ILLUMINA NA 175 TRUE +EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_2 Homo sapiens hg19 chr7 55249005 55249131 + CAGCGTGGACAACCCCCACGTGT 0 GTGTGTGCAGATCGCAAAGGTAATCA 0 + ILLUMINA NA 177 TRUE +EGFR54 EGFR54.chr7.55259514.55259524 EGFR54.chr7.55259514.55259524_tile_1 Homo sapiens hg19 chr7 55259514 55259524 - CCTCCCCTGCATGTGTTAAACAATACA 0 CCAAAATCTGTGATCTTGACATGCTGC 0 - ILLUMINA NA 178 TRUE +MET1 MET1.chr7.116339642.116339642 MET1.chr7.116339642.116339642_tile_1 Homo sapiens hg19 chr7 116339642 116339642 - CCTTCTCACTGATATCGAATGCAATGG 0 CTTCTATCTGTGGGGAGAATATGCAGT 0 - ILLUMINA NA 180 TRUE +MET2 MET2.chr7.116340262.116340262 MET2.chr7.116340262.116340262_tile_1 Homo sapiens hg19 chr7 116340262 116340262 - GCCCTGGATATTCTTTTTGAGACTGAT 0 GAAGAAGTCGTTGACATATTTGATAGG 0 - ILLUMINA NA 188 TRUE +MET3 MET3.chr7.116411990.116411990 MET3.chr7.116411990.116411990_tile_1 Homo sapiens hg19 chr7 116411990 116411990 - TGCAAAACCAAAAATAAACAACAATGTC 0 TTACACTTCGGGCACTTACAAGCCTA 0 - ILLUMINA NA 171 TRUE +MET4 MET4.chr7.116417463.116417464 MET4.chr7.116417463.116417464_tile_1 Homo sapiens hg19 chr7 116417463 116417464 - CACAAGGGGAAAGTGTAAATCAACGTTT 0 CACAACCAAAATGCCCTGTGCAAAAGA 0 - ILLUMINA NA 191 TRUE +MET6 MET6.chr7.116423413.116423474 MET6.chr7.116423413.116423474_tile_1 Homo sapiens hg19 chr7 116423413 116423474 - GAGGAGAAACTCAGAGATAACCAATAC 0 TGTCTCTGGCAAGACCAAAATCAGCA 0 - ILLUMINA NA 172 TRUE +SMO1 SMO1.chr7.128845101.128845101 SMO1.chr7.128845101.128845101_tile_1 Homo sapiens hg19 chr7 128845101 128845101 - TGACCAGGGTGAAGAGCGTGCAGAG 0 AAGGGCACTTCGCACTGGCCTGAA 0 - ILLUMINA NA 186 TRUE +SMO2 SMO2.chr7.128846040.128846040 SMO2.chr7.128846040.128846040_tile_1 Homo sapiens hg19 chr7 128846040 128846040 - ATTGCCACAGTGAGGACAAAGGGGAGT 0 GTACACGATGACAAAGATGATGACGCA 0 - ILLUMINA NA 186 TRUE +SMO3 SMO3.chr7.128846374.128846374 SMO3.chr7.128846374.128846374_tile_1 Homo sapiens hg19 chr7 128846374 128846374 - TAGCTGGGGTTTCAGCATGGGGGCAGC 0 AAGCCCGCACGGTATCGGTAGTTCT 0 - ILLUMINA NA 190 TRUE +SMO4 SMO4.chr7.128850341.128850341 SMO4.chr7.128850341.128850341_tile_1 Homo sapiens hg19 chr7 128850341 128850341 - AACCACTGACCAAGGCTGTGCTAGAGG 0 TCATGGCGATGCCAGTTCCAAACA 0 - ILLUMINA NA 190 TRUE +SMO5 SMO5.chr7.128851593.128851593 SMO5.chr7.128851593.128851593_tile_1 Homo sapiens hg19 chr7 128851593 128851593 - TTCAGATCCTCTGGGGCCTTTCCTTC 0 AGAAATATCCTGGGGCAGTATGGCTCC 0 - ILLUMINA NA 173 TRUE +BRAF1 BRAF1.chr7.140453121.140453193 BRAF1.chr7.140453121.140453193_tile_1 Homo sapiens hg19 chr7 140453121 140453193 - ACCTAAACTCTTCATAATGCTTGCTCT 0 GGTCCCATCAGTTTGAACAGTTGTCT 0 - ILLUMINA NA 176 TRUE +BRAF28 BRAF28.chr7.140481397.140481478 BRAF28.chr7.140481397.140481478_tile_1 Homo sapiens hg19 chr7 140481397 140481478 - GGTTTTCTTTTTCTGTTTGGCTTGACT 0 CTACAAGGGAAAGTGGCATGGTAAGTA 0 - ILLUMINA NA 178 TRUE +FGFR1_1 FGFR1_1.chr8.38282209.38282209 FGFR1_1.chr8.38282209.38282209_tile_1 Homo sapiens hg19 chr8 38282209 38282209 - TTTTGAGAGGCTTGGGCTCAGCAGAA 0 TCACCGGCCCATCCTGCAAGCAGGG 0 - ILLUMINA NA 179 TRUE +FGFR1_2 FGFR1_2.chr8.38285938.38285938 FGFR1_2.chr8.38285938.38285938_tile_1 Homo sapiens hg19 chr8 38285938 38285938 - AAGAGATCATCACTAAGGGAGCAGTGG 0 GGATGATGATGATGATGATGACTCCTC 0 - ILLUMINA NA 184 TRUE +JAK2_1 JAK2_1.chr9.5073769.5073770 JAK2_1.chr9.5073769.5073770_tile_1 Homo sapiens hg19 chr9 5073769 5073770 - TTCAGTTTCAAAAATACTTAACTCCTGTT 0 CTCCATAATTTAAAACCAAATGCTTGTG 0 - ILLUMINA NA 188 TRUE +CDKN2A1 CDKN2A1.chr9.21971153.21971187 CDKN2A1.chr9.21971153.21971187_tile_1 Homo sapiens hg19 chr9 21971153 21971187 - TTGTGTGGGGGTCTGCTTGGCGGTGA 0 AACTGCGCCGACCCCGCCACTCTCA 0 - ILLUMINA NA 187 TRUE +ABL1_1 ABL1_1.chr9.133738330.133738364 ABL1_1.chr9.133738330.133738364_tile_1 Homo sapiens hg19 chr9 133738330 133738364 - ATGCATCGCCTAATGCCAGCAGACGC 0 TGATGTCCGTGCGTTCCATCTCCCAC 0 - ILLUMINA NA 191 TRUE +ABL1_9 ABL1_9.chr9.133747520.133747520 ABL1_9.chr9.133747520.133747520_tile_1 Homo sapiens hg19 chr9 133747520 133747520 - AGCGCCTGTGTCACCCTGGGGGT 0 AAAACGAAGGTGAAATTATTTCAGGAA 0 - ILLUMINA NA 190 TRUE +ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_1 Homo sapiens hg19 chr9 133748283 133748414 + AGAATCCTTCAGAAGGCTTTTTCTTTAGAC 0 AACCTCCTGGACTACCTGAGGGAGT 0 + ILLUMINA NA 172 TRUE +ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_2 Homo sapiens hg19 chr9 133748283 133748414 - TCCATGGCGCAGGCTGCCTGGCC 0 CCGTAGGTCATGAACTCAGTGATGA 0 - ILLUMINA NA 182 TRUE +ABL1_16 ABL1_16.chr9.133750356.133750356 ABL1_16.chr9.133750356.133750356_tile_1 Homo sapiens hg19 chr9 133750356 133750356 - GGGAAGAGCAAGAAAGAGGCAGAAAAA 0 TGTGTAGGTGTCCCCTGTCATCAA 0 - ILLUMINA NA 190 TRUE +NOTCH1_1 NOTCH1_1.chr9.139397768.139397768 NOTCH1_1.chr9.139397768.139397768_tile_1 Homo sapiens hg19 chr9 139397768 139397768 - AGACCTGGCTTCCCACCACCCCAGGCT 0 AGATTGACAACCGGCAGTGTGTGCAG 0 - ILLUMINA NA 190 TRUE +NOTCH1_2 NOTCH1_2.chr9.139399344.139399422 NOTCH1_2.chr9.139399344.139399422_tile_1 Homo sapiens hg19 chr9 139399344 139399422 - AGTGCGAGTGGGACGGGCTGGACTGT 0 ACACCAACGTGGTCTTCAAGCGTGAC 0 - ILLUMINA NA 171 TRUE +RET1 RET1.chr10.43609078.43609104 RET1.chr10.43609078.43609104_tile_1 Homo sapiens hg19 chr10 43609078 43609104 - ACTCGCCTCCCAGCAATTTCCTCCC 0 TTGCAGGTGCCATAGCCAGCTTTAAT 0 - ILLUMINA NA 180 TRUE +RET2_9 RET2_9.chr10.43609940.43609950 RET2_9.chr10.43609940.43609950_tile_1 Homo sapiens hg19 chr10 43609940 43609950 + AAGCCTCACACCACCCCCACCCACAGAT 0 CCCATCTCCTCAGCTGAGATGACCTT 0 + ILLUMINA NA 175 TRUE +RET10 RET10.chr10.43613840.43613840 RET10.chr10.43613840.43613840_tile_1 Homo sapiens hg19 chr10 43613840 43613840 - AGAACAGGGCTGTATGGAGCCCCCAGC 0 GGGAGGCGTTCTCTGAAATGCAG 0 - ILLUMINA NA 190 TRUE +RET11_12 RET11_12.chr10.43615567.43615569 RET11_12.chr10.43615567.43615569_tile_1 Homo sapiens hg19 chr10 43615567 43615569 - ATGGTGCACCTGGGATCCCTGGGAG 0 ATGTTTCTGGCTGCCAAGTCCCGATGAA 0 - ILLUMINA NA 172 TRUE +RET13 RET13.chr10.43617416.43617416 RET13.chr10.43617416.43617416_tile_1 Homo sapiens hg19 chr10 43617416 43617416 - AATTCCCTGGCCAAGCTGCACAGACGG 0 CCATTTAACTGGAATCCGACCCTAAAG 0 - ILLUMINA NA 178 TRUE +PTEN1 PTEN1.chr10.89624242.89624244 PTEN1.chr10.89624242.89624244_tile_1 Homo sapiens hg19 chr10 89624242 89624244 - TACGGACATTTTCGCATCCGTCTACTC 0 ATGATGGCTGTCATGTCTGGGAGCCTG 0 - ILLUMINA NA 176 TRUE +PTEN3 PTEN3.chr10.89685307.89685307 PTEN3.chr10.89685307.89685307_tile_1 Homo sapiens hg19 chr10 89685307 89685307 - TGGACTTCTTGACTTAATCGGTTTAGG 0 CTTGTAATGGTTTTTATGCTTTGAATCCA 0 - ILLUMINA NA 186 TRUE +PTEN4 PTEN4.chr10.89711893.89711900 PTEN4.chr10.89711893.89711900_tile_1 Homo sapiens hg19 chr10 89711893 89711900 - GGATGAGAATTTCAAGCACTTACTGCA 0 TGGGAATAGTTACTCCCTGGTGGACA 0 - ILLUMINA NA 176 TRUE +PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_1 Homo sapiens hg19 chr10 89717615 89717772 - GGGTCCTGAATTGGAGGAATATATCTTCAC 0 ACACGAAATATGGATTCTGTATCTGC 0 - ILLUMINA NA 181 TRUE +PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_2 Homo sapiens hg19 chr10 89717615 89717772 + CAGTTTGTGGTCTGCCAGCTAAA 0 AAAGGTTTGTACTTTACTTTCATTGGGAG 0 + ILLUMINA NA 188 TRUE +PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_1 Homo sapiens hg19 chr10 89720716 89720852 - AATTTGGAGAAAAGTATCGGTTGGCTT 0 AGGTTTCCTCTGGTCCTGGTATGAA 0 - ILLUMINA NA 188 TRUE +PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_2 Homo sapiens hg19 chr10 89720716 89720852 + AAAATGATCTTGACAAAGCAAATAAAGAC 0 CTTGCTTGACAAGTTTTTAACTTATGTATT 0 + ILLUMINA NA 179 TRUE +FGFR2_1 FGFR2_1.chr10.123258034.123258034 FGFR2_1.chr10.123258034.123258034_tile_1 Homo sapiens hg19 chr10 123258034 123258034 - CTAACAGTAGCTGCCCATGAGTTAGAG 0 TTCTTGGAGCCTGCACACAGGATGGTG 0 - ILLUMINA NA 180 TRUE +FGFR2_2 FGFR2_2.chr10.123274774.123274803 FGFR2_2.chr10.123274774.123274803_tile_1 Homo sapiens hg19 chr10 123274774 123274803 - GCCTTTTGGTTCCTTTGGTTGTGCTAT 0 CATAGGGGTCTTCTTAATCGCCTGTAT 0 - ILLUMINA NA 186 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_1 Homo sapiens hg19 chr10 123279503 123279677 - CACGTGGAAAAGAACGGCAGTAAATAC 0 GGAGTTGAGAGAGGATGATTCTCTTTT 0 - ILLUMINA NA 172 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_2 Homo sapiens hg19 chr10 123279503 123279677 + TTTAGATTCAGAAAGTCCTCACCTTGAG 0 CTCCTCCGACCACTGTGGAGGCATTT 0 + ILLUMINA NA 171 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_3 Homo sapiens hg19 chr10 123279503 123279677 - ACTGACAGCCCTCTGGACAACACAGCT 0 CGTAGAGTTTGTCTGCAAGGTTTACAG 0 - ILLUMINA NA 184 TRUE +HRAS1 HRAS1.chr11.533873.533875 HRAS1.chr11.533873.533875_tile_1 Homo sapiens hg19 chr11 533873 533875 - TACCAGGGAGAGGCTGGCTGTGTGAAC 0 AGTACAGCGCCATGCGGGACCAGTAC 0 - ILLUMINA NA 180 TRUE +HRAS6 HRAS6.chr11.534285.534289 HRAS6.chr11.534285.534289_tile_1 Homo sapiens hg19 chr11 534285 534289 - CTGCCCTGTGGGGCCTGGGGCTGG 0 AAGAGTGCGCTGACCATCCAGCTGATC 0 - ILLUMINA NA 185 TRUE +ATM1 ATM1.chr11.108117847.108117848 ATM1.chr11.108117847.108117848_tile_1 Homo sapiens hg19 chr11 108117847 108117848 - GAAAGGAATAGTTGCATGTACAGAGTC 0 GATATCTGCCATCAATTCAATCAAATTTT 0 - ILLUMINA NA 174 TRUE +ATM2 ATM2.chr11.108119823.108119823 ATM2.chr11.108119823.108119823_tile_1 Homo sapiens hg19 chr11 108119823 108119823 - TTGCTAGTAATAGGTTTGGGGGTAGAC 0 GATCAAAATCATTCTGTGACTTCTGAA 0 - ILLUMINA NA 172 TRUE +ATM3 ATM3.chr11.108123551.108123551 ATM3.chr11.108123551.108123551_tile_1 Homo sapiens hg19 chr11 108123551 108123551 - AAGCTATAGCTTAAAATGATAAAGAGCAT 0 ACAAAGAAAAACAAAAAGCTTCACTTAGA 0 - ILLUMINA NA 172 TRUE +ATM4 ATM4.chr11.108137973.108138003 ATM4.chr11.108137973.108138003_tile_1 Homo sapiens hg19 chr11 108137973 108138003 - ACTGCCAAATCAATATAAAGAAGTAAAAGA 0 GATTTCCATTAGTATCATCTTCCATTGAT 0 - ILLUMINA NA 189 TRUE +ATM6 ATM6.chr11.108155132.108155132 ATM6.chr11.108155132.108155132_tile_1 Homo sapiens hg19 chr11 108155132 108155132 - TCGAATAAATAGCCTTAAAACTTAAAGGTT 0 ATCCCACTGTCTCTGGTACCCTCATAG 0 - ILLUMINA NA 179 TRUE +ATM7 ATM7.chr11.108170476.108170479 ATM7.chr11.108170476.108170479_tile_1 Homo sapiens hg19 chr11 108170476 108170479 - ACTCACCAATCTTCTACCAGTGTGTTA 0 ACTTCTCCCAAGCAGCTTCCAACAGCC 0 - ILLUMINA NA 178 TRUE +ATM9 ATM9.chr11.108172421.108172421 ATM9.chr11.108172421.108172421_tile_1 Homo sapiens hg19 chr11 108172421 108172421 - ACAGAACTGTTTTAGATATGCTGGGTA 0 AATGTTTTTCAAACAGGTAACAGCTGC 0 - ILLUMINA NA 182 TRUE +ATM10 ATM10.chr11.108173640.108173640 ATM10.chr11.108173640.108173640_tile_1 Homo sapiens hg19 chr11 108173640 108173640 - CAGGTCATAAACAAGGAATTATATCAGACT 0 ATATCATCCAGGCCTTCAAAAGGG 0 - ILLUMINA NA 191 TRUE +ATM11 ATM11.chr11.108180945.108180945 ATM11.chr11.108180945.108180945_tile_1 Homo sapiens hg19 chr11 108180945 108180945 - CCCTTATTGAGACAATGCCAACATTAA 0 CTAGATAATTTAAATCCAGCCAGAAAGC 0 - ILLUMINA NA 188 TRUE +ATM12 ATM12.chr11.108200958.108200961 ATM12.chr11.108200958.108200961_tile_1 Homo sapiens hg19 chr11 108200958 108200961 - CAAAGTCGGAATACCCACATATCATGT 0 CCTTTACTGTGTATCTTGCATAGAATAAT 0 - ILLUMINA NA 172 TRUE +ATM14 ATM14.chr11.108204681.108204681 ATM14.chr11.108204681.108204681_tile_1 Homo sapiens hg19 chr11 108204681 108204681 - TAGGTTGAAACATATGAAATTTGCCAA 0 GGGACAACAACATCTTCTAAATTCTTAAG 0 - ILLUMINA NA 174 TRUE +ATM15 ATM15.chr11.108205769.108205769 ATM15.chr11.108205769.108205769_tile_1 Homo sapiens hg19 chr11 108205769 108205769 - GACAAAATCCCAAATAAAGCAGAAAGAA 0 CCTGCTAAGCGAAATTCTGCTTTAAATG 0 - ILLUMINA NA 191 TRUE +ATM16 ATM16.chr11.108206594.108206594 ATM16.chr11.108206594.108206594_tile_1 Homo sapiens hg19 chr11 108206594 108206594 - CACCCAACCAAATGGCATCTTTTATAT 0 TTGTCTCAGGTCATCACGGCCCTTCAG 0 - ILLUMINA NA 186 TRUE +ATM17 ATM17.chr11.108218089.108218089 ATM17.chr11.108218089.108218089_tile_1 Homo sapiens hg19 chr11 108218089 108218089 - CTAGGACAACTGTTTATGCTGAAAACA 0 TCTATATGTACAAGTTCTGCTGACTGC 0 - ILLUMINA NA 188 TRUE +ATM18 ATM18.chr11.108225590.108225590 ATM18.chr11.108225590.108225590_tile_1 Homo sapiens hg19 chr11 108225590 108225590 - GCTAAGTGCACAATCTCCTCCTTTCT 0 AACAGAGTTTCCTGAGAGTTTCTCATC 0 - ILLUMINA NA 191 TRUE +ATM19 ATM19.chr11.108236086.108236203 ATM19.chr11.108236086.108236203_tile_1 Homo sapiens hg19 chr11 108236086 108236203 - TGAAGATCACACCCAAGCTTTCCATC 0 TCAGCTACTTTGTTGAAACTCTGGTCA 0 - ILLUMINA NA 185 TRUE +KRAS1 KRAS1.chr12.25378562.25378562 KRAS1.chr12.25378562.25378562_tile_1 Homo sapiens hg19 chr12 25378562 25378562 - TCTTTCCCAGAGAACAAATTAAAAGAGT 0 AGACAAGACAGGTAAGTAACACTGAAA 0 - ILLUMINA NA 187 TRUE +KRAS2 KRAS2.chr12.25380275.25380283 KRAS2.chr12.25380275.25380283_tile_1 Homo sapiens hg19 chr12 25380275 25380283 - TTGTTGTTGAGTTGTATATAACACCTTTT 0 AGTACAGTGCAATGAGGGACCAGTAC 0 - ILLUMINA NA 184 TRUE +KRAS7 KRAS7.chr12.25398255.25398285 KRAS7.chr12.25398255.25398285_tile_1 Homo sapiens hg19 chr12 25398255 25398285 - GGTACTGGTGGAGTATTTGATAGTGTAT 0 GCTAATTCAGAATCATTTTGTGGACGAAT 0 - ILLUMINA NA 191 TRUE +PTPN11_1 PTPN11_1.chr12.112888163.112888211 PTPN11_1.chr12.112888163.112888211_tile_1 Homo sapiens hg19 chr12 112888163 112888211 - TACTGACCTTTCAGAGGTAGGATCTGC 0 GTGTTCTGAATCTTGATGTGGGTGAC 0 - ILLUMINA NA 190 TRUE +PTPN11_10 PTPN11_10.chr12.112926884.112926888 PTPN11_10.chr12.112926884.112926888_tile_1 Homo sapiens hg19 chr12 112926884 112926888 - CAAGAGGCCTAGCAAGAGAATGAGAAT 0 TCTGAGACCGCACCATCTGGATGGTT 0 - ILLUMINA NA 178 TRUE +HNF1A_1 HNF1A_1.chr12.121431413.121431414 HNF1A_1.chr12.121431413.121431414_tile_1 Homo sapiens hg19 chr12 121431413 121431414 - TTGCCGCAGCCCAGACCAAACCAGCA 0 TTGAAACGGTTCCTCCGCCCCTTCTT 0 - ILLUMINA NA 175 TRUE +HNF1A_3 HNF1A_3.chr12.121432070.121432070 HNF1A_3.chr12.121432070.121432070_tile_1 Homo sapiens hg19 chr12 121432070 121432070 - ACATACCACTTACCGTGGACCTTACT 0 CGGTTGGCAAACCAGTTGTAGACA 0 - ILLUMINA NA 181 TRUE +FLT3_1 FLT3_1.chr13.28592620.28592653 FLT3_1.chr13.28592620.28592653_tile_1 Homo sapiens hg19 chr13 28592620 28592653 - CACATCACAGTAAATAACACTCTGGTG 0 TTGTCAGGGGCAATGTGAGGCTGCTATT 0 - ILLUMINA NA 178 TRUE +FLT3_13 FLT3_13.chr13.28602329.28602329 FLT3_13.chr13.28602329.28602329_tile_1 Homo sapiens hg19 chr13 28602329 28602329 - ACTTGAGTTTTACATTTTTAATGCTCCT 0 TGTCAGGTAACCCACTTCCACGAAAA 0 - ILLUMINA NA 171 TRUE +FLT3_14 FLT3_14.chr13.28608244.28608341 FLT3_14.chr13.28608244.28608341_tile_1 Homo sapiens hg19 chr13 28608244 28608341 - CTATCTGCAGAACTGCCTATTCCTAAC 0 TTCCAAGAGAAAATTTAGAGTTTGGTAAG 0 - ILLUMINA NA 190 TRUE +FLT3_22 FLT3_22.chr13.28610138.28610138 FLT3_22.chr13.28610138.28610138_tile_1 Homo sapiens hg19 chr13 28610138 28610138 + CCAGGTCCAAGATGGTAATGGGTAT 0 ATACCAATACTTTGTGAAGCCAAGGTGG 0 + ILLUMINA NA 171 TRUE +RB1_1 RB1_1.chr13.48919244.48919244 RB1_1.chr13.48919244.48919244_tile_1 Homo sapiens hg19 chr13 48919244 48919244 - CCTTTCCAATTTGCTGAAGAGTGCAAA 0 CAGTAACCTTAAAAATTTGTGTTATTTCGT 0 - ILLUMINA NA 182 TRUE +RB1_2 RB1_2.chr13.48923148.48923148 RB1_2.chr13.48923148.48923148_tile_1 Homo sapiens hg19 chr13 48923148 48923148 - GCTAACAGTTAATAAGCCAAGCAGAGA 0 AAATGTGATCCAAGAAACTTTTAGCAC 0 - ILLUMINA NA 178 TRUE +RB1_3 RB1_3.chr13.48942685.48942685 RB1_3.chr13.48942685.48942685_tile_1 Homo sapiens hg19 chr13 48942685 48942685 - ACATAAAGAAACGTGAACAAATCTGAAA 0 GGTGTTCTCTGTGTTTCAAAACTAAATAA 0 - ILLUMINA NA 173 TRUE +RB1_4 RB1_4.chr13.48955538.48955550 RB1_4.chr13.48955538.48955550_tile_1 Homo sapiens hg19 chr13 48955538 48955550 - TTCCCTATATGTTCTTGAGGTAGATGT 0 AATGTTTTATCATTTCTCTTGTCAAGTTG 0 - ILLUMINA NA 182 TRUE +RB1_6 RB1_6.chr13.49027168.49027168 RB1_6.chr13.49027168.49027168_tile_1 Homo sapiens hg19 chr13 49027168 49027168 - TTTGCAGTTTGAATGGTCAACATAACA 0 TAAAGGTGAATCCTATATGAAACATGATG 0 - ILLUMINA NA 178 TRUE +RB1_7 RB1_7.chr13.49033843.49033846 RB1_7.chr13.49033843.49033846_tile_1 Homo sapiens hg19 chr13 49033843 49033846 - GAAGTGCTTGATTTTCTTACTTGGTCC 0 TAGGCTAGCCGATACACTGTGGGAATA 0 - ILLUMINA NA 178 TRUE +RB1_8 RB1_8.chr13.49037877.49037877 RB1_8.chr13.49037877.49037877_tile_1 Homo sapiens hg19 chr13 49037877 49037877 - GGAAAATTACCTACCTCCTGAACAGCA 0 AGTAGTCAGAATTTTATTACATGGTTTTGT 0 - ILLUMINA NA 172 TRUE +RB1_9 RB1_9.chr13.49039164.49039164 RB1_9.chr13.49039164.49039164_tile_1 Homo sapiens hg19 chr13 49039164 49039164 - TGTTTTGGTGGACCCATTACATTAGAT 0 CTTTGATCAAAACACGTTTGAATGTCT 0 - ILLUMINA NA 174 TRUE +AKT1 AKT1.chr14.105246455.105246455 AKT1.chr14.105246455.105246455_tile_1 Homo sapiens hg19 chr14 105246455 105246455 - TCTGACGGGTAGAGTGTGCGTGGCTC 0 GCTCCCCTCAACAACTTCTCTGTG 0 - ILLUMINA NA 173 TRUE +CDH1_1 CDH1_1.chr16.68835649.68835650 CDH1_1.chr16.68835649.68835650_tile_1 Homo sapiens hg19 chr16 68835649 68835650 - GGCGGTGGTGGTGCCCCACTGT 0 CTTTGAATCGGGTGTCGAGGGAAAAA 0 - ILLUMINA NA 171 TRUE +CDH1_2 CDH1_2.chr16.68846137.68846137 CDH1_2.chr16.68846137.68846137_tile_1 Homo sapiens hg19 chr16 68846137 68846137 - ACATTCTCTAGTCTGGAGAGAGTTTTC 0 TTGGTGTCAGTGACTGTGATCACAGCT 0 - ILLUMINA NA 176 TRUE +CDH1_3 CDH1_3.chr16.68847274.68847277 CDH1_3.chr16.68847274.68847277_tile_1 Homo sapiens hg19 chr16 68847274 68847277 - CATCTTGCCAGGTACCATACAAACCTT 0 CACTTTCAGTGTGGTGATTACGACGTT 0 - ILLUMINA NA 178 TRUE +TP53_1 TP53_1.chr17.7574003.7574021 TP53_1.chr17.7574003.7574021_tile_1 Homo sapiens hg19 chr17 7574003 7574021 - ACTAAATGCATGTTGCTTTTGTACCGT 0 AGAGCTGAATGAGGCCTTGGAACTC 0 - ILLUMINA NA 172 TRUE +TP53_3 TP53_3.chr17.7577022.7577129 TP53_3.chr17.7577022.7577129_tile_1 Homo sapiens hg19 chr17 7577022 7577129 - ATCCTGAGTAGTGGTAATCTACTGGGA 0 AGGTAAGCAAGCAGGACAAGAAGCG 0 - ILLUMINA NA 172 TRUE +TP53_17 TP53_17.chr17.7577523.7577574 TP53_17.chr17.7577523.7577574_tile_1 Homo sapiens hg19 chr17 7577523 7577574 - AAAAAGGCCTCCCCTGCTTGCCACAGG 0 ATCATCACACTGGAAGACTCCAGGTCA 0 - ILLUMINA NA 190 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_1 Homo sapiens hg19 chr17 7578190 7578536 - TTTGGATGACAGAAACACTTTTCGACA 0 CCTGCTGCTTATTTGACCTCCCTATAAC 0 - ILLUMINA NA 172 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_2 Homo sapiens hg19 chr17 7578190 7578536 + GACCCCAGTTGCAAACCAGACCTCA 0 TGAGGAATCAGAGGCCTGGGGA 0 + ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_3 Homo sapiens hg19 chr17 7578190 7578536 - TTGTGAGGCGCTGCCCCCACCATGAG 0 GCATCTTATCCGAGTGGAAGGAAATTTG 0 - ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_4 Homo sapiens hg19 chr17 7578190 7578536 + CGTCTCTCCAGCCCCAGCTGCTCACCAT 0 CCACAGCTGCACAGGGCAGGTCTT 0 + ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_5 Homo sapiens hg19 chr17 7578190 7578536 - GCATGTTTGTTTCTTTGCTGCCGTCT 0 TTGATTCCACACCCCCGCCCGGC 0 - ILLUMINA NA 179 TRUE +TP53_60 TP53_60.chr17.7579358.7579403 TP53_60.chr17.7579358.7579403_tile_1 Homo sapiens hg19 chr17 7579358 7579403 - AGATGAAGCTCCCAGAATGCCAGAGG 0 TTCTTGCATTCTGGGACAGCCAAGTCT 0 - ILLUMINA NA 185 TRUE +TP53_64 TP53_64.chr17.7579882.7579882 TP53_64.chr17.7579882.7579882_tile_1 Homo sapiens hg19 chr17 7579882 7579882 - ATGGTGTTGGGGGAGGGGGTTCCTTCT 0 CCCCTCTGAGTCAGGAAACATTTTCAG 0 - ILLUMINA NA 182 TRUE +ERBB2_1 ERBB2_1.chr17.37880219.37880261 ERBB2_1.chr17.37880219.37880261_tile_1 Homo sapiens hg19 chr17 37880219 37880261 - CATATCTCCCCAAACCCCAATGAAGAG 0 CTTTGATGGCCACTGGAATTTTCACA 0 - ILLUMINA NA 172 TRUE +ERBB2_4 ERBB2_4.chr17.37880993.37881012 ERBB2_4.chr17.37880993.37881012_tile_1 Homo sapiens hg19 chr17 37880993 37881012 - ATACACCAGTTCAGCAGGTCCTGGGAG 0 TATGCTTCCTGGGGACAAGGGTAC 0 - ILLUMINA NA 190 TRUE +ERBB2_13 ERBB2_13.chr17.37881332.37881440 ERBB2_13.chr17.37881332.37881440_tile_1 Homo sapiens hg19 chr17 37881332 37881440 - TCTGCTCCTTGGTCCTTCACCTAACCT 0 ACATCCTCCAGGTAGCTCATCCCCTGG 0 - ILLUMINA NA 186 TRUE +SMAD4_1 SMAD4_1.chr18.48575169.48575170 SMAD4_1.chr18.48575169.48575170_tile_1 Homo sapiens hg19 chr18 48575169 48575170 - TACAAAAATTGAAACACTATTGAGATCCT 0 CGCATACTGACAATATTTAACATGTTTTAG 0 - ILLUMINA NA 172 TRUE +SMAD4_2 SMAD4_2.chr18.48581198.48581198 SMAD4_2.chr18.48581198.48581198_tile_1 Homo sapiens hg19 chr18 48581198 48581198 - ATGTTGGGAAAGTTGGCAGTGCTGGTA 0 CAAAGTCATGCACATATTCATCCTTCAC 0 - ILLUMINA NA 180 TRUE +SMAD4_3 SMAD4_3.chr18.48584560.48584560 SMAD4_3.chr18.48584560.48584560_tile_1 Homo sapiens hg19 chr18 48584560 48584560 - GCTGTCTAAAAATTAAGGCCCACATGG 0 TGATGCTATCTGCAACAGTCCTTCAC 0 - ILLUMINA NA 188 TRUE +SMAD4_4 SMAD4_4.chr18.48586262.48586262 SMAD4_4.chr18.48586262.48586262_tile_1 Homo sapiens hg19 chr18 48586262 48586262 - ACTCATGTCATGATGAGTATTGTACTC 0 AATGCAAGCTCATTGTGAACAGGCCCT 0 - ILLUMINA NA 184 TRUE +SMAD4_5 SMAD4_5.chr18.48591826.48591919 SMAD4_5.chr18.48591826.48591919_tile_1 Homo sapiens hg19 chr18 48591826 48591919 - CAATACCTTGCTCTCTCAATGGCTTCT 0 AGTAAGCAATGGAACACCAATACTCAG 0 - ILLUMINA NA 188 TRUE +SMAD4_11 SMAD4_11.chr18.48593405.48593405 SMAD4_11.chr18.48593405.48593405_tile_1 Homo sapiens hg19 chr18 48593405 48593405 - GCACTTGGGTAGATCTTATGAACAGCA 0 TGCCTATGTGCAACCTTAGGAAGAAA 0 - ILLUMINA NA 172 TRUE +SMAD4_12 SMAD4_12.chr18.48603032.48603094 SMAD4_12.chr18.48603032.48603094_tile_1 Homo sapiens hg19 chr18 48603032 48603094 - AAAGAATGAAAAGCATACTTACTGATAGC 0 CTGACGCAAATCAAAGACCTTTTAAGAA 0 - ILLUMINA NA 172 TRUE +SMAD4_15 SMAD4_15.chr18.48604668.48604754 SMAD4_15.chr18.48604668.48604754_tile_1 Homo sapiens hg19 chr18 48604668 48604754 - GCATGGTATGAAGTACTTCGTCTAGGA 0 AAGGTCATCAACACCAATTCCAGCAG 0 - ILLUMINA NA 172 TRUE +STK11_1 STK11_1.chr19.1207021.1207092 STK11_1.chr19.1207021.1207092_tile_1 Homo sapiens hg19 chr19 1207021 1207092 - CGCAACTTCTTCTTCTTGAGGATCTTG 0 TAGATGACCTCGGTGGAGTCGATGCGG 0 - ILLUMINA NA 178 TRUE +STK11_4 STK11_4.chr19.1220487.1220502 STK11_4.chr19.1220487.1220502_tile_1 Homo sapiens hg19 chr19 1220487 1220502 - AAAGCCGGGGAGCCCTGGCTGGTC 0 AGATTTTGAGGGTGCCACCGGTGGTG 0 - ILLUMINA NA 181 TRUE +STK11_8 STK11_8.chr19.1221264.1221319 STK11_8.chr19.1221264.1221319_tile_1 Homo sapiens hg19 chr19 1221264 1221319 + TGTACCCCTTCGAAGGGGACAACATCTA 0 GCTTTTGTGCAGAAATGTAGGGTTGG 0 + ILLUMINA NA 177 TRUE +STK11_12 STK11_12.chr19.1223059.1223125 STK11_12.chr19.1223059.1223125_tile_1 Homo sapiens hg19 chr19 1223059 1223125 - ACATCCTGGCCGAGTCAGCAGAGCC 0 ACCGGTCCTTGGTGTCTGGGCTC 0 - ILLUMINA NA 188 TRUE +JAK3_1 JAK3_1.chr19.17945696.17945696 JAK3_1.chr19.17945696.17945696_tile_1 Homo sapiens hg19 chr19 17945696 17945696 - ATCCCTGATCCCACTTTCATTCCCTCA 0 ATGCCCATCAGTGCCCTGGATCCTG 0 - ILLUMINA NA 176 TRUE +JAK3_2 JAK3_2.chr19.17948009.17948009 JAK3_2.chr19.17948009.17948009_tile_1 Homo sapiens hg19 chr19 17948009 17948009 - TAGTGCTGTGTGCACTAATGGCAGACT 0 AGCTTGATGAGCCAAGTGTCGTAC 0 - ILLUMINA NA 190 TRUE +SRC SRC.chr20.36031762.36031762 SRC.chr20.36031762.36031762_tile_1 Homo sapiens hg19 chr20 36031762 36031762 - AAAGAGGAAGGGCCTCGCCCCTGGCAAT 0 TACTGGGGCTCGGTGGACGTGAAGTAG 0 - ILLUMINA NA 191 TRUE +GNAS1 GNAS1.chr20.57484420.57484421 GNAS1.chr20.57484420.57484421_tile_1 Homo sapiens hg19 chr20 57484420 57484421 - ACAGCTGGTTATTCCAGAGGGACTGGG 0 GCGAAGCAGGTCCTGAAACAAAATTGA 0 - ILLUMINA NA 172 TRUE +SMARCB1_1 SMARCB1_1.chr22.24133967.24133990 SMARCB1_1.chr22.24133967.24133990_tile_1 Homo sapiens hg19 chr22 24133967 24133990 - GCGAGTGGTTTTGAAACAGGTTTACA 0 ACATACGGAGGTAGTTTCCCACCTAT 0 - ILLUMINA NA 189 TRUE +SMARCB1_3 SMARCB1_3.chr22.24143240.24143240 SMARCB1_3.chr22.24143240.24143240_tile_1 Homo sapiens hg19 chr22 24143240 24143240 - TTGTGGGGAGCACAAGGTCAAAGCAG 0 ATGCGGTTCCTGTTGATGGTTGTGGA 0 - ILLUMINA NA 175 TRUE +SMARCB1_4 SMARCB1_4.chr22.24145582.24145582 SMARCB1_4.chr22.24145582.24145582_tile_1 Homo sapiens hg19 chr22 24145582 24145582 - ATGTCCTGCGTGTCAGGTCCAGAATCT 0 TTCTGCCCATCGATCTCCATGTCCAG 0 - ILLUMINA NA 176 TRUE +SMARCB1_5_6 SMARCB1_5_6.chr22.24176352.24176357 SMARCB1_5_6.chr22.24176352.24176357_tile_1 Homo sapiens hg19 chr22 24176352 24176357 - ACTCCACCCCCACCCGATCCTCAGGA 0 TGTTGGCAAGACGCCTCATCCGCCTGG 0 - ILLUMINA NA 173 TRUE +GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_1 Homo sapiens hg19 chr19 3114942 3115070 + AGTGCGCGGTCCACCCCCTCCT 0 CTGCCCACCCAGCAGGACGTGCT 0 + ILLUMINA NA 182 TRUE +GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_2 Homo sapiens hg19 chr19 3114942 3115070 - CGGCACACCGGGCAAATGAGCC 0 TAGCCCAAGGTGGCGATGCGGTC 0 - ILLUMINA NA 177 TRUE +GNA11_5 GNA11_5.chr19.3118922.3119051 GNA11_5.chr19.3118922.3119051_tile_1 Homo sapiens hg19 chr19 3118922 3119051 + TCCTGCTCCAGCCGATGTCAGTCT 0 GATCCACTGCTTTGAGAACGTGACAT 0 + ILLUMINA NA 189 TRUE +GNA11_6 GNA11_6.chr19.3119204.3119357 GNA11_6.chr19.3119204.3119357_tile_2 Homo sapiens hg19 chr19 3119204 3119357 + GGATGGAGGAGAGCAAAGCCCTGTT 0 CATGGGGAGGGGCTCGCGGGCA 0 + ILLUMINA NA 189 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_1 Homo sapiens hg19 chr19 3120987 3121177 - AACATCTTCAGGATGAACTCCCGCGCC 0 ACGGCCCACCCAGCTCGACCCCC 0 - ILLUMINA NA 172 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_2 Homo sapiens hg19 chr19 3120987 3121177 + AGGTCCCCAGCGGGACGCCCAG 0 CAGCTCAACCTCAAGGAGTACAACCT 0 + ILLUMINA NA 187 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_3 Homo sapiens hg19 chr19 3120987 3121177 - AAAAATCTCCTCCCGCGGGCAGAG 0 AGGATGGTGTCCTTCACGGCCGC 0 - ILLUMINA NA 185 TRUE +GNAQ_4 GNAQ_4.chr9.80412436.80412564 GNAQ_4.chr9.80412436.80412564_tile_1 Homo sapiens hg19 chr9 80412436 80412564 - CATTCTCATTGTGTCTTCCCTCCTCTA 0 GTAACTGAGTCCATGAAACCTATTTCC 0 - ILLUMINA NA 188 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_1 Homo sapiens hg19 chr9 80409379 80409508 - GCTTAGTGAATATGATCAAGTTCTCGTGG 0 GCTTTCTTGAAATTTGATTTTAGGACTTTT 0 - ILLUMINA NA 174 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_2 Homo sapiens hg19 chr9 80409379 80409508 + AGATAATAAAATGATAATCCATTGCCTGTC 0 TTGGCCCCCTACATCGACCATTCT 0 + ILLUMINA NA 177 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_3 Homo sapiens hg19 chr9 80409379 80409508 - ATTGAATTGACTTGGATGATCATCGTC 0 GGTCAGAGAGAAGAAAATGGATACACT 0 - ILLUMINA NA 182 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_1 Homo sapiens hg19 chr9 80343430 80343583 - GAAAATCATGTATTCCCATCTAGTCGACT 0 TTGCCCTGTGCAGCCTGCGTGTTGA 0 - ILLUMINA NA 172 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_2 Homo sapiens hg19 chr9 80343430 80343583 + TTCACAGCTACTGAGCTGTGGTATGA 0 AGGGGTATGTGATAATTGTTCTAAAGAGAG 0 + ILLUMINA NA 171 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_3 Homo sapiens hg19 chr9 80343430 80343583 - GGTCGTATACAAAAGATGGGTTGGACTTAT 0 GTTCCAGAACTCCTCGGTTATTCTGTT 0 - ILLUMINA NA 187 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_1 Homo sapiens hg19 chr9 80336240 80336429 - ACCATCCTCCAGTTGAACCTGAAGG 0 TTTATTGCCGTCCTGGACTCTGTGTGAGCG 0 - ILLUMINA NA 172 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_2 Homo sapiens hg19 chr9 80336240 80336429 + CAGGGAAGGGCAGGGCGGGTGTCTA 0 ATAATTTTGTCACTGTCTGGGTTCAGG 0 + ILLUMINA NA 172 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_3 Homo sapiens hg19 chr9 80336240 80336429 - CCAATGATGATTGAATACATTAGCAGAT 0 TACTCCCACTTCACGTGCGCCACAGAC 0 - ILLUMINA NA 177 TRUE +[Targets] +TargetA TargetB Target Number Chromosome Start Position End Position Probe Strand Sequence Species Build ID +MPL1_2.chr1.43815008.43815009_tile_1 MPL1_2.chr1.43815008.43815009_tile_1 1 chr1 43814982 43815163 + GGTGGCAGTTTCCTGCACACTACAGGTACCGCCCCCGCCAGGCAGGAGACTGGCGGTGGACCAGGTGGAGCCGAAGGCCTGTAAACAGGCATTCTTGGTTCGCTCTGTGACCCCAGATCTCCGTCCACCGCC Homo sapiens hg19 +NRAS1_7.chr1.115256528.115256531_tile_1 NRAS1_7.chr1.115256528.115256531_tile_1 1 chr1 115256500 115256680 + TCTTGTCCAGCTGTATCCAGTATGTCCAACAAACAGGTTTCACCATCTATAACCACTTGTTTTCTGTAAGAATCCTGGGGGTGTGGAGGGTAAGGGGGCAGGGAGGGAGGGAAGTTCAATTTTTATTA Homo sapiens hg19 +NRAS8_13.chr1.115258730.115258748_tile_1 NRAS8_13.chr1.115258730.115258748_tile_1 1 chr1 115258702 115258884 + TGCGCTTTTCCCAACACCACCTGCTCCAACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGAGCCACATCTACAGTACTTTAAAG Homo sapiens hg19 +ALK1.chr2.29432664.29432664_tile_1 ALK1.chr2.29432664.29432664_tile_1 1 chr2 29432636 29432822 + TCGGGCCATCCCGAAGTCTCCAATCTTGGCCACTCTTCCAGGGCCTGGACAGGTCAAGAGGCAGTTTCTGGCAGCAATGTCTCTGGGAAGAAAGGAAATGCATTTCCTAATTTTATCCCTAGGAAGATGAGTG Homo sapiens hg19 +ALK2.chr2.29443695.29443695_tile_1 ALK2.chr2.29443695.29443695_tile_1 1 chr2 29443667 29443836 + GTTGAATTTGCTGCAGAGCAGAGAGGGATGTAACCAAAATTAACTGAGCTGAGTCTGGGCAAATCTTAAACTGGGAGGAACAGGATACAAAGTTACATTTTCAGCAGCTACAATGTATA Homo sapiens hg19 +IDH1_1_2.chr2.209113112.209113113_tile_1 IDH1_1_2.chr2.209113112.209113113_tile_1 1 chr2 209113084 209113264 + ACGACCTATGATGATAGGTTTTACCCATCCACTCACAAGCCGGGGGATATTTTTGCAGATAATGGCTTCTCTGAAGACCGTGCCACCCAGAATATTTCGTATGGTGCCATTTGGTGATTTCCACATT Homo sapiens hg19 +ERBB4_1_2.chr2.212288942.212288955_tile_1 ERBB4_1_2.chr2.212288942.212288955_tile_1 1 chr2 212288912 212289100 + CCTTTCTCTAATAAATCAGGGATTTCTCGCGTTGGAATTCCATCATAGGGTTTTCCTCCAAAGGTCATCAGTTCCCATATAGTAACTCCTATATTGGAGAAAAAATTCTTACTTAAGCATATTAACAACATATGT Homo sapiens hg19 +ERBB4_3_4.chr2.212530066.212530135_tile_1 ERBB4_3_4.chr2.212530066.212530135_tile_1 1 chr2 212530036 212530210 + TGGATGGCATGGGTGGCACTCCCGATCTGGATCAGCATACTTGAAAATGAAACTGTTTGCCCCCTGTAAGCCATCTGGACATTTTTCCACACAGTTTGGGCCATCTTTAAAATGAGAGCACT Homo sapiens hg19 +ERBB4_5.chr2.212576857.212576857_tile_1 ERBB4_5.chr2.212576857.212576857_tile_1 1 chr2 212576821 212576990 + AATCCACAGTCTGAGCTGACATCAATGATCCTGTGCCAATGCCATCACAAGCTGTAGAAACAAGACTCAGAGTTAGGGGATTGAGAAACTTATTTTTGGCCAATAAATCA Homo sapiens hg19 +ERBB4_6_7.chr2.212578341.212578349_tile_1 ERBB4_6_7.chr2.212578341.212578349_tile_1 1 chr2 212578315 212578499 + CGCACACAAGAACTGGAATCTACCACAAAGTTATCTGATTAAAAAAAAAAAAAAGGTAAAATAAGCATTAATGTTAACATTCAGCAAACAAGCTCAAAACAAGATATTTTAGGGTTTAAAAATGATTAGCA Homo sapiens hg19 +ERBB4_8.chr2.212587147.212587147_tile_1 ERBB4_8.chr2.212587147.212587147_tile_1 1 chr2 212587115 212587285 + CTCCATATGTGTACTTTGCATTGAAATTGTGCTCCAGTTGAAAGGTGGTTGGATTGTAGACAAAGGTTTGGGGACACTGAGTAACACATGCTCCACTGTCATTGAAATTCATGCAGG Homo sapiens hg19 +ERBB4_9.chr2.212589811.212589811_tile_1 ERBB4_9.chr2.212589811.212589811_tile_1 1 chr2 212589783 212589957 + TGTGTCCTTAGGTCCTGAGCAGCCTCCAGCACATTCTCGATGGCAGCAGTCACTGACGTAAGGTCCGTAGCATCTGCCGTCACATTGTTCTGCACACACCGTCCTTGTCACTGCAGAAGAC Homo sapiens hg19 +ERBB4_10.chr2.212652764.212652764_tile_1 ERBB4_10.chr2.212652764.212652764_tile_1 1 chr2 212652706 212652876 + ATAATTCTACTTACATCCTGAACTACCATTTGTTGACACAAGAGTCAAGTTGGAAGGCCATGGGTTCCGAACAATATCTTGCCAATGAATGGTGTCTGCATAACAAAGGAATTT Homo sapiens hg19 +ERBB4_11.chr2.212812157.212812157_tile_1 ERBB4_11.chr2.212812157.212812157_tile_1 1 chr2 212812127 212812311 + TGTCAAGTTCTTTAATCCAAGTTCTTGAAGTCCAAAGTTTCCATCTTTTCTGTAGTTTAAAAATATTGCCAAGGCATATCGATCCTCATAAAGTTTTGTCCCACGAATAATGCGTAAATTCTCCAGAGG Homo sapiens hg19 +VHL1_2.chr3.10183797.10183817_tile_1 VHL1_2.chr3.10183797.10183817_tile_1 1 chr3 10183769 10183952 + GGCTCAACTTCGACGGCGAGCCGCAGCCCTACCCAACGCTGCCGCCTGGCACGGGCCGCCGCATCCACAGCTACCGAGGTACGGGCCCGGCGCTTAGGCCCGACCCAGCAGGGACGATAGCACGGTCTGAAGC Homo sapiens hg19 +VHL3_5.chr3.10188245.10188301_tile_1 VHL3_5.chr3.10188245.10188301_tile_1 1 chr3 10188217 10188401 + GGTTAACCAAACTGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATTTTTGCCAATATCACACTGCCAGGTACTGACGTTTTACTTTTTAAAAAGATAAGGTTGTTGTGGTAAGTACAGGATA Homo sapiens hg19 +VHL6_8.chr3.10191480.10191506_tile_1 VHL6_8.chr3.10191480.10191506_tile_1 1 chr3 10191450 10191634 + TCTGAAAGAGCGATGCCTCCAGGTTGTCCGGAGCCTAGTCAAGCCTGAGAATTACAGGAGACTGGACATCGTCAGGTCGCTCTACGAAGATCTGGAAGACCACCCAAATGTGCAGAAAGACCTGGAGCGG Homo sapiens hg19 +MLH1.chr3.37067240.37067240_tile_1 MLH1.chr3.37067240.37067240_tile_1 1 chr3 37067212 37067394 + GGTTCGTACAGATTCCCGGGAACAGAAGCTTGATGCATTTCTGCAGCCTCTGAGCAAACCCCTGTCCAGTCAGCCCCAGGCCATTGTCACAGAGGATAAGACAGATATTTCTAGTGGCAGGGCTAGGCAG Homo sapiens hg19 +CTNNB1_1_16.chr3.41266040.41266137_tile_1 CTNNB1_1_16.chr3.41266040.41266137_tile_1 1 chr3 41266010 41266180 + ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGC Homo sapiens hg19 +PIK3CA1.chr3.178916876.178916876_tile_1 PIK3CA1.chr3.178916876.178916876_tile_1 1 chr3 178916836 178917024 + TGATGAAACAAGACGACTTTGTGACCTTCGGCTTTTTCAACCCTTTTTAAAAGTAATTGAACCAGTAGGCAACCGTGAAGAAAAGATCCTCAATCGAGAAATTGGTATGATACAATATCCTATTCTAAAATGCAAA Homo sapiens hg19 +PIK3CA2.chr3.178921553.178921553_tile_1 PIK3CA2.chr3.178921553.178921553_tile_1 1 chr3 178921525 178921709 + ATGTAAATATTCGAGACATTGATAAGGTAAAGTCAAATGCTGATGCTTATTATTTTATAGAAATTATTTTAGATAACCTTTTTCTTGCACTATACAGTAATCTGTTGACCTGTAGTATGTTTTCAGATGGT Homo sapiens hg19 +PIK3CA3.chr3.178927980.178927980_tile_1 PIK3CA3.chr3.178927980.178927980_tile_1 1 chr3 178927906 178928082 + TTATAATTTAGACTAGTGAATATTTTTCTTTGTTTTTTAAGGAACACTGTCCATTGGCATGGGGAAATATAAACTTGTTTGATTACACAGACACTCTAGTATCTGGAAAAATGGCTTTGAATC Homo sapiens hg19 +PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 1 chr3 178936044 178936214 + ATCCTCTCTCTGAAATCACTGAGCAGGAGAAAGATTTTCTATGGAGTCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGAATTTGG Homo sapiens hg19 +PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 1 chr3 178938832 178939004 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTCTCAAACAGGAGAAGAAGGATGAAACACAAAAGGTGTGTGACTCTAGTTTGTGTTTGAGACTCTT Homo sapiens hg19 +PIK3CA13_20.chr3.178952007.178952150_tile_1 PIK3CA13_20.chr3.178952007.178952150_tile_1 1 chr3 178951881 178952054 + TATCTAGCTATTCGACAGCATGCCAATCTCTTCATAAATCTTTTCTCAATGATGCTTGGCTCTGGAATGCCAGAACTACAATCTTTTGATGACATTGCATACATTCGAAAGACCCTAGCC Homo sapiens hg19 +PIK3CA13_20.chr3.178952007.178952150_tile_2 PIK3CA13_20.chr3.178952007.178952150_tile_2 1 chr3 178951999 178952184 - TTTCAGTTCAATGCATGCTGTTTAATTGTGTGGAAGATCCAATCCATTTTTGTTGTCCAGCCACCATGATGTGCATCATTCATTTGTTTCATGAAATACTCCAAAGCCTCTTGCTCAGTTTTATCTAAG Homo sapiens hg19 +FGFR3_1_2.chr4.1803564.1803568_tile_1 FGFR3_1_2.chr4.1803564.1803568_tile_1 1 chr4 1803538 1803712 + GCGCTCCCCGCACCGGCCCATCCTGCAGGCGGGGCTGCCGGCCAACCAGACGGCGGTGCTGGGCAGCGACGTGGAGTTCCACTGCAAGGTGTACAGTGACGCACAGCCCCACATCCAGTGGCT Homo sapiens hg19 +FGFR3_3_4.chr4.1806119.1806153_tile_1 FGFR3_3_4.chr4.1806119.1806153_tile_1 1 chr4 1806091 1806277 + CGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTA Homo sapiens hg19 +FGFR3_5_7.chr4.1807862.1807890_tile_1 FGFR3_5_7.chr4.1807862.1807890_tile_1 1 chr4 1807836 1808025 + CCGGGACGTGCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGGGCCGGCTGCCCGTGA Homo sapiens hg19 +FGFR3_8.chr4.1808331.1808331_tile_1 FGFR3_8.chr4.1808331.1808331_tile_1 1 chr4 1808295 1808464 + GCTCCCCGTACCCCGGCATCCCTGTGGAGGAGCTCTTCAAGCTGCTGAAGGAGGGCCACCGCATGGACAAGCCCGCCAACTGCACACACGACCTGTGAGTGGCATCCCTGGCCCTCCACTGGGTCC Homo sapiens hg19 +FGFR3_9.chr4.1808949.1808949_tile_1 FGFR3_9.chr4.1808949.1808949_tile_1 1 chr4 1808921 1809105 + CCTGCTGCCCCCGGCCCCACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAATGTGAGGGGTCCCTAGCAGCCCACCCTGCTGCTGGTGCACAGCCACTCCCCGGCATGAGACTCAGTGC Homo sapiens hg19 +PDGFRA1_4.chr4.55141013.55141049_tile_1 PDGFRA1_4.chr4.55141013.55141049_tile_1 1 chr4 55140981 55141157 + AAACCGAGGTATGAAATTCGCTGGAGGGTCATTGAATCAATCAGCCCAGATGGACATGAATATATTTATGTGGACCCGATGCAGCTGCCTTATGACTCAAGATGGGAGTTTCCAAGAGATGGA Homo sapiens hg19 +PDGFRA5.chr4.55144146.55144146_tile_1 PDGFRA5.chr4.55144146.55144146_tile_1 1 chr4 55144120 55144306 + AACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGG Homo sapiens hg19 +PDGFRA6.chr4.55144547.55144547_tile_1 PDGFRA6.chr4.55144547.55144547_tile_1 1 chr4 55144519 55144703 + CACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATGAAAGCAC Homo sapiens hg19 +PDGFRA7_23.chr4.55152040.55152109_tile_1 PDGFRA7_23.chr4.55152040.55152109_tile_1 1 chr4 55152012 55152184 + CGTCCTCCTGGCACAAGGAAAAATTGTGAAGATCTGTGACTTTGGCCTGGCCAGAGACATCATGCATGATTCGAACTATGTGTCGAAAGGCAGTGTACGTCCTCACTTCCCTCACTGGTCA Homo sapiens hg19 +KIT1.chr4.55561764.55561764_tile_1 KIT1.chr4.55561764.55561764_tile_1 1 chr4 55561736 55561913 + CGACGAGATTAGGCTGTTATGCACTGATCCGGGCTTTGTCAAATGGACTTTTGAGATCCTGGATGAAACGAATGAGAATAAGCAGAATGAATGGATCACGGAAAAGGCAGAAGCCACCAACACCG Homo sapiens hg19 +KIT2.chr4.55592185.55592186_tile_1 KIT2.chr4.55592185.55592186_tile_1 1 chr4 55592155 55592341 + CCTATTTTAACTTTGCATTTAAAGGTAACAACAAAGGTATATTTCTTTTTAATCCAATTTAAGGGGATGTTTAGGCTCTGTCTACCATATCAGTCATGATTTTAAGTTCATTCCAACATTGACCATGTCATTTC Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_1 KIT3_19.chr4.55593464.55593689_tile_1 1 chr4 55593342 55593512 + ATTTCTCTTCCATTGTAGAGCAAATCCATCCCCACACCCTGTTCACTCCTTTGCTGATTGGTTTCGTAATCGTAGCTGGCATGATGTGCATTATTGTGATGATTCTGACCTACAAATA Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_2 KIT3_19.chr4.55593464.55593689_tile_2 1 chr4 55593436 55593609 - TTCTGTGGGGAGAAAGGGAAAAATAGATCACCTTTTAATAATTATTGTCTCAGTCATTAGAGCACTCTGGAGAGAGAACAAATAAATGGTTACCTGTAAATATTTGTAGGTCAGAATCATCA Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_3 KIT3_19.chr4.55593464.55593689_tile_3 1 chr4 55593556 55593739 + AACCCATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTCAG Homo sapiens hg19 +KIT20_21.chr4.55594221.55594258_tile_1 KIT20_21.chr4.55594221.55594258_tile_1 1 chr4 55594193 55594380 + CAAAGTCCTGAGTTACCTTGGTAATCACATGAATATTGTGAATCTACTTGGAGCCTGCACCATTGGAGGTAAAGCCGTGTCCAAGCTGCCTTTTATTGTCTGTCAGGTTATCAAAACATGACATTTTAATATG Homo sapiens hg19 +KIT22.chr4.55595519.55595519_tile_1 KIT22.chr4.55595519.55595519_tile_1 1 chr4 55595493 55595675 + CAGAATATTGTTGCTATGGTGATCTTTTGAATTTTTTGAGAAGAAAACGTGATTCATTTATTTGTTCAAAGCAGGAAGATCATGCAGAAGCTGCACTTTATAAGAATCTTCTGCATTCAAAGGAGTCT Homo sapiens hg19 +KIT23.chr4.55597495.55597497_tile_1 KIT23.chr4.55597495.55597497_tile_1 1 chr4 55597467 55597652 + CAGCGATAGTACTAATGAGTACATGGACATGAAACCTGGAGTTTCTTATGTTGTCCCAACCAAGGCCGACAAAAGGAGATCTGTGAGAATAGGTGAGTACCTACCTATCAAGCAACCAAGAGTAACTTTAC Homo sapiens hg19 +KIT24_28.chr4.55599320.55599348_tile_1 KIT24_28.chr4.55599320.55599348_tile_1 1 chr4 55599290 55599472 + AGAGACATCAAGAATGATTCTAATTATGTGGTTAAAGGAAACGTGAGTACCCATTCTCTGCTTGACAGTCCTGCAAAGGATTTTTAGTTTCAACTTTCGATAAAAATTGTTTCCTGTGATTTTCATAAT Homo sapiens hg19 +KIT29.chr4.55602694.55602694_tile_1 KIT29.chr4.55602694.55602694_tile_1 1 chr4 55602666 55602850 + CCTGAAAGCATTTTCAACTGTGTATACACGTTTGAAAGTGACGTCTGGTCCTATGGGATTTTTCTTTGGGAGCTGTTCTCTTTAGGTAAAATGATCCTTGCCAAAGACAACTTCATTAGACTCAGAGCATCTT Homo sapiens hg19 +KDR1.chr4.55946114.55946257_tile_1 KDR1.chr4.55946114.55946257_tile_1 1 chr4 55945984 55946155 + CGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCT Homo sapiens hg19 +KDR1.chr4.55946114.55946257_tile_2 KDR1.chr4.55946114.55946257_tile_2 1 chr4 55946098 55946284 - GGATATCACTCCGATGACACAGACACCACCGTGTACTCCAGTGAGGAAGCAGAACTTTTAAAGCTGATAGAGATTGGAGTGCAAACCGGTAGCACAGCCCAGATTCTCCAGCCTGACTCGGGGACCACACTGA Homo sapiens hg19 +KDR3.chr4.55953807.55953807_tile_1 KDR3.chr4.55953807.55953807_tile_1 1 chr4 55953777 55953965 + TTGGGGTCACATACTTCCTCCTCCTCCATACAGGAAACAGGTGAGGTAGGCAGAGAGAGTCCAGAATCCTCTTCCATGCTCAAAGTCTCTGATATCGGAAGAACAATGTAGTCTTTGCCATCCTGAAACAATAAA Homo sapiens hg19 +KDR4.chr4.55955111.55955127_tile_1 KDR4.chr4.55955111.55955127_tile_1 1 chr4 55955085 55955257 + CCCCGTGCCAGCAGTCCAGCATGGTCTGGTACCTAGAGAAGCAAAACACTGATTTCATTAAATGCCTCTTTCTTCCTGAATGCTGAAAATAAGCACTTAAATGAGTACACATTTGTAAAGAG Homo sapiens hg19 +KDR6.chr4.55960989.55961023_tile_1 KDR6.chr4.55960989.55961023_tile_1 1 chr4 55960959 55961129 + TCACTGAGGGACTTCTCCTCCACAAATCCAGAGCTGGCTGAGCTCTGGCTACTGGTGATGCTGTCCAAGCGCCGTTTCAGATCCACAGGGATTGCTCCAACGTAGTCTTTCCCTTGA Homo sapiens hg19 +KDR8.chr4.55962507.55962507_tile_1 KDR8.chr4.55962507.55962507_tile_1 1 chr4 55962477 55962653 + GCTCCTTCTACAAATACAGTACAAAGAGGGAAATCATAGGTATGGACATTTCCTTCAATAATTGGGGTCCCTCCCTCCCTGCATGCCACTATACAACTTACCCTCCGGGGTAACACAGCTGTGA Homo sapiens hg19 +KDR9.chr4.55972964.55972964_tile_1 KDR9.chr4.55972964.55972964_tile_1 1 chr4 55972936 55973106 + ACTGAGACAGCTTGGCTATAAGAAAGAGATAACAGCGCATATTATGATTTAATTTTTCTTTAATTAGAGTCAAGAGTAAGGAAAAGATTCAGACTTTGGTTATTCTGTTCTTAGAAA Homo sapiens hg19 +KDR10.chr4.55979623.55979623_tile_1 KDR10.chr4.55979623.55979623_tile_1 1 chr4 55979595 55979775 + CTCGGTTTACAAGTTTCTTATGCTGATGCTGAAAAAAAGAGTTGACTGAACTTCCAAAGCACAGCATATAACATTACCCAATAACTTCTAGTAACACACAGAATTAAATCTGGGCTTTGGTAAACATT Homo sapiens hg19 +KDR11.chr4.55980348.55980348_tile_1 KDR11.chr4.55980348.55980348_tile_1 1 chr4 55980320 55980496 + TGCTGTACAATTTAAGACAAGCTTTTCTCCAACAGATAGTTCAATTCCATGAGACGGACTCAGAACCACATCATAAATCCTATACCCTAGAGCAAGTAAATTGAAAAAACAGAACATGAGAGA Homo sapiens hg19 +FBXW7_1.chr4.153245446.153245446_tile_1 FBXW7_1.chr4.153245446.153245446_tile_1 1 chr4 153245416 153245604 + AACGACTGGTGCCCTGTTAACGTGTGAATGCAATTCCCTGTCTCCACATCCCAAACACGGATTGATGTATCAAGAGATCCACTCACCACATGGATACCATCAAACTACAAAAGACACAGTTTATTAGAATAGA Homo sapiens hg19 +FBXW7_2.chr4.153247288.153247366_tile_1 FBXW7_2.chr4.153247288.153247366_tile_1 1 chr4 153247248 153247417 + TTGAACACAGCGGACTGCTGCAACATGACCCATCAAAACATGTAAACACTGGCCTGTCTCAATATCCCAAACCCTAAGAGTGGCATCTCGAGAACCGCTAACAACTCTGCAG Homo sapiens hg19 +FBXW7_5.chr4.153249384.153249384_tile_1 FBXW7_5.chr4.153249384.153249384_tile_1 1 chr4 153249338 153249520 + TTCATGAAGATGCATACAACGCACAGTGGAAGTATGCCCATATAAGGTGTGTATACATTCTCCAGTCTCTGCATTCCACACTTTGAGTGTCCGATCTGTAGATCCACTAATGATGATGTTGTCTCTCAT Homo sapiens hg19 +FBXW7_7.chr4.153250883.153250883_tile_1 FBXW7_7.chr4.153250883.153250883_tile_1 1 chr4 153250853 153251031 + ATTCGGTTACCACAAAACTGTAAGCATGTGATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGA Homo sapiens hg19 +FBXW7_8.chr4.153258983.153258983_tile_1 FBXW7_8.chr4.153258983.153258983_tile_1 1 chr4 153258953 153259142 + TCGTTGAAACTGGGGTTCTATCACTTGCATCATATGTTTTACTTGTGTTGGTTCACAACTATCAATGAGTTCATCTAAAGCAAGCAATTTCTCTGGTCCACTCCAGCTCTATCAAAGAGAATTAGAAATTTT Homo sapiens hg19 +APC1.chr5.112173917.112173917_tile_1 APC1.chr5.112173917.112173917_tile_1 1 chr5 112173887 112174071 + AAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGA Homo sapiens hg19 +APC2.chr5.112174631.112174631_tile_1 APC2.chr5.112174631.112174631_tile_1 1 chr5 112174603 112174775 + TCGAGTGGGTTCTAATCATGGAATTAATCAAAATGTAAGCCAGTCTTTGTGTCAAGAAGATGACTATGAAGATGATAAGCCTACCAATTATAGTGAACGTTACTCTGAAGAAGAACAGC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_1 APC3_42.chr5.112175162.112175958_tile_1 1 chr5 112175034 112175208 - TCTGCTTCCTGTGTCGTCTGATTACATCCTATTTCATCTTCAGCTGATGACAAAGATGATAATGAACTACATCTTGAAAAACATATTGGAGTATCTTCTACACAATAAGTCTGTATTGTT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_2 APC3_42.chr5.112175162.112175958_tile_2 1 chr5 112175128 112175297 + ATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCAC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_3 APC3_42.chr5.112175162.112175958_tile_3 1 chr5 112175216 112175386 - CCTGAAGAAAATTCAACAGCTTTGTGCCTGGCTGATTCTGAAGATAAACTAGAACCCTGCAGTCTGCTGGATTTGGTTCTAGGGTGCTGTGACACTGCTGGAACTTCGCTCACAGGAT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_4 APC3_42.chr5.112175162.112175958_tile_4 1 chr5 112175306 112175475 + CACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_5 APC3_42.chr5.112175162.112175958_tile_5 1 chr5 112175394 112175566 - GCCACTTACCATTCCACTGCATGGTTCACTCTGAACGGAGCTGGCAATCGAACGACTCTCAAAACTATCAAGTGAACTGACAGAAGTACATCTGCTAAACATGAGTGGGGTCTCCTGAAC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_6 APC3_42.chr5.112175162.112175958_tile_6 1 chr5 112175512 112175683 + GCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_7 APC3_42.chr5.112175162.112175958_tile_7 1 chr5 112175630 112175799 - CCGTGGCAAAATGTAATAAAGTATCAGCATCTGGAAGAACCTGGACCCTCTGAACTGCAGCATTTACTGCAGCTTGCTTAGGTCCACTCTCTCTCTTTTCAGCAGTAGGTGCTTT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_8 APC3_42.chr5.112175162.112175958_tile_8 1 chr5 112175740 112175911 + GGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_9 APC3_42.chr5.112175162.112175958_tile_9 1 chr5 112175854 112176042 - AGTATTTCAATATCATCATCATCTGAATCATCTAATAGGTCCTTTTCAGAATCAATAGTTTTTTCTGCCTCTTTCTCTTGGTTTTCATTTGATTCTTTAGGCTGCTCTGATTCTGTTTCATTCCCATTGTCATTT Homo sapiens hg19 +CSF1R1_3.chr5.149433644.149433646_tile_1 CSF1R1_3.chr5.149433644.149433646_tile_1 1 chr5 149433616 149433799 + GATAGTTGTTGGGCTGCAGCAAGGGCTGGGCGATATCCCCTTGCTCGCAGCAGGTCAGGTGCTCACTAGAGCTCTCCTCCTCCAGCTCACTGCTGCTGCTGCCGCTGCCACCGCTTCTGCTGCTGCTCGGC Homo sapiens hg19 +CSF1R4.chr5.149453044.149453044_tile_1 CSF1R4.chr5.149453044.149453044_tile_1 1 chr5 149453016 149453189 + CAAGTAGGCACTCTCTGGAAAGCAGAACACACAAGCATCTGGCATTAGTGGGAAGATGTCCTTGTTTATTTGTCCATTTTGTCATCCACCCATTGATCCAGTCCCTGAGCAGCTATGTCAC Homo sapiens hg19 +NPM1.chr5.170837547.170837548_tile_1 NPM1.chr5.170837547.170837548_tile_1 1 chr5 170837493 170837677 + TTTTTTTTCCAGGCTATTCAAGATCTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAGTTTAAACAATTTGTTAAAAAATTTTCCGTCTTATTTCATTTCTGTAACAGTTGATATCTGGCTGTCCTTTTTA Homo sapiens hg19 +EGFR1.chr7.55211080.55211080_tile_1 EGFR1.chr7.55211080.55211080_tile_1 1 chr7 55211052 55211238 + AGAGGAAATATGTACTACGAAAATTCCTATGCCTTAGCAGTCTTATCTAACTATGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTACAGGGTGAGAGGCTGGGATGCCAAGGCTGGGGGT Homo sapiens hg19 +EGFR2.chr7.55221822.55221822_tile_1 EGFR2.chr7.55221822.55221822_tile_1 1 chr7 55221792 55221964 + GGTGCCACCTGCGTGAAGAAGTGTCCCCGTGAGTCCTCCTCTGTGGGCCCTCTAACTGGTCAGGCATCCTTGTCCCGCTCTGTCTCCTGCTGAGCCCTGGAGTATCCCATCTTGGAGAGT Homo sapiens hg19 +EGFR3.chr7.55233043.55233043_tile_1 EGFR3.chr7.55233043.55233043_tile_1 1 chr7 55233019 55233203 + GGAGTCATGGGAGAAAACAACACCCTGGTCTGGAAGTACGCAGACGCCGGCCATGTGTGCCACCTGTGCCATCCAAACTGCACCTACGGGTGAGTGGAAAGTGAAGGAGAACAGAACATTTCCTCTCTTGCAAAT Homo sapiens hg19 +EGFR4.chr7.55241677.55241708_tile_1 EGFR4.chr7.55241677.55241708_tile_1 1 chr7 55241649 55241827 + AGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAGGTAAGGTCCCTGGCACAGGCCTCTGGGCTGGGCCGCAGGGCCTCTCATGGTCTGGTGGGGAGCC Homo sapiens hg19 +EGFR9.chr7.55242418.55242511_tile_1 EGFR9.chr7.55242418.55242511_tile_1 1 chr7 55242388 55242576 + GACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCT Homo sapiens hg19 +EGFR44.chr7.55249005.55249131_tile_1 EGFR44.chr7.55249005.55249131_tile_1 1 chr7 55248879 55249052 + TCTTCACCTGGAAGGGGTCCATGTGCCCCTCCTTCTGGCCACCATGCGAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTG Homo sapiens hg19 +EGFR44.chr7.55249005.55249131_tile_2 EGFR44.chr7.55249005.55249131_tile_2 1 chr7 55249003 55249178 - CAGTTGAGCAGGTACTGGGAGCCAATATTGTCTTTGTGTTCCCGGACATAGTCCAGGAGGCAGCCGAAGGGCATGAGCTGCGTGATGAGCTGCACGGTGGAGGTGAGGCAGATGCCCAGCAGGCGGC Homo sapiens hg19 +EGFR54.chr7.55259514.55259524_tile_1 EGFR54.chr7.55259514.55259524_tile_1 1 chr7 55259486 55259662 + GCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTAAGGAGGTGGCTTTAGGTCAGCCAGCATTTTCCTGACACCAGGGACCAGGCTGCCTTCCCACTAGC Homo sapiens hg19 +MET1.chr7.116339642.116339642_tile_1 MET1.chr7.116339642.116339642_tile_1 1 chr7 116339614 116339792 + AGCCCAGCCAGTGTCCTGACTGTGTGGTGAGCGCCCTGGGAGCCAAAGTCCTTTCATCTGTAAAGGACCGGTTCATCAACTTCTTTGTAGGCAATACCATAAATTCTTCTTATTTCCCAGATCAT Homo sapiens hg19 +MET2.chr7.116340262.116340262_tile_1 MET2.chr7.116340262.116340262_tile_1 1 chr7 116340234 116340420 + AACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGAGCACTGCTTTAATAGGGTAAGTCACATCAGTTCCCCACTTATAAACTGTGAGGTATAAATTAGAAATAAGT Homo sapiens hg19 +MET3.chr7.116411990.116411990_tile_1 MET3.chr7.116411990.116411990_tile_1 1 chr7 116411958 116412127 + GCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATATACCTCAGTGGGTTGT Homo sapiens hg19 +MET4.chr7.116417463.116417464_tile_1 MET4.chr7.116417463.116417464_tile_1 1 chr7 116417431 116417620 + TATATCATGGGACTTTGTTGGACAATGATGGCAAGAAAATTCACTGTGCTGTGAAATCCTTGAACAGTAAGTGGCATTTTATTTAACCATGGAGTATACTTTTGTGGTTTGCAACCTAATAAATAGCTTATAATA Homo sapiens hg19 +MET6.chr7.116423413.116423474_tile_1 MET6.chr7.116423413.116423474_tile_1 1 chr7 116423385 116423555 + TGTATGATAAAGAATACTATAGTGTACACAACAAAACAGGTGCAAAGCTGCCAGTGAAGTGGATGGCTTTGGAAAGTCTGCAAACTCAAAAGTTTACCACCAAGTCAGATGTGGTAAT Homo sapiens hg19 +SMO1.chr7.128845101.128845101_tile_1 SMO1.chr7.128845101.128845101_tile_1 1 chr7 128845073 128845257 + GGTTCGGACAGACAACCCCAAGAGCTGGTACGAGGACGTGGAGGGCTGCGGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCACCAGGACATGCACAGCTACATCGCGGCCTTCGGGGCCGTCACGGGC Homo sapiens hg19 +SMO2.chr7.128846040.128846040_tile_1 SMO2.chr7.128846040.128846040_tile_1 1 chr7 128846010 128846194 + TACGCCCTGATGGCTGGTGTGGTTTGGTTTGTGGTCCTCACCTATGCCTGGCACACTTCCTTCAAAGCCCTGGGCACCACCTACCAGCCTCTCTCGGGCAAGACCTCCTACTTCCACCTGCTCACCTGGTC Homo sapiens hg19 +SMO3.chr7.128846374.128846374_tile_1 SMO3.chr7.128846374.128846374_tile_1 1 chr7 128846348 128846536 + CGTGCTGGCCCCAATCGGCCTGGTGCTCATCGTGGGAGGCTACTTCCTCATCCGAGGTGAGTGAAGACCAGGCCAGGACCAGTTGGGCAACAAAATATACTGGGCACTTGCTGCCAGTACTGGGAGCTGCCAGCACG Homo sapiens hg19 +SMO4.chr7.128850341.128850341_tile_1 SMO4.chr7.128850341.128850341_tile_1 1 chr7 128850311 128850499 + GCACCTGGGTCTGGACCAAGGCCACGCTGCTCATCTGGAGGCGTACCTGGTGCAGGTGGGCATGGCAGCCAGCCCCTCCTGCCCTGCCCGCCTCACCCTCAGCCTTGGGACCCCATCTTTAGGTTTTGTCGGGTCCTG Homo sapiens hg19 +SMO5.chr7.128851593.128851593_tile_1 SMO5.chr7.128851593.128851593_tile_1 1 chr7 128851563 128851734 + GTCACCCCTGTGGCAACTCCAGGTATGAGAGTTCAAGCTTCTGGAGGAAGGTGGGGGGAGCACAGAGGCTGGGGGCTTCTGGGACTGGAGTACAGGGGCTGTCGGAGGAGGAGGAAGAG Homo sapiens hg19 +BRAF1.chr7.140453121.140453193_tile_1 BRAF1.chr7.140453121.140453193_tile_1 1 chr7 140453093 140453267 + CACTCCATCGAGATTTCACTGTAGCTAGACCAAAATCACCTATTTTTACTGTGAGGTCTTCATGAAGAAATATATCTGAGGTGTAGTAAGTAAAGGAAAACAGTAGATCTCATTTTCCTATC Homo sapiens hg19 +BRAF28.chr7.140481397.140481478_tile_1 BRAF28.chr7.140481397.140481478_tile_1 1 chr7 140481369 140481545 + ACTGTTCCAAATGATCCAGATCCAATTCTTTGTCCCACTGTAATCTGCCCATCAGGAATCTCCCAATCATCACTCGAGTCCCGTCTACCAAGTGTTTTCTTGATAAAAACAGTAAAAAAGTCA Homo sapiens hg19 +FGFR1_1.chr8.38282209.38282209_tile_1 FGFR1_1.chr8.38282209.38282209_tile_1 1 chr8 38282183 38282360 + GGGGACCGCTCTGTGGAAGATGGGAGAGGAGGCACTTGTCATGGGGACCTTGCCATGGCTAAAGAGGGGTGGGCTCACCTGCGCCCCACTTGGCTTTCCCAGTGATGGGTTGTAAACCTCCCAGCAC Homo sapiens hg19 +FGFR1_2.chr8.38285938.38285938_tile_1 FGFR1_2.chr8.38285938.38285938_tile_1 1 chr8 38285908 38286090 + TCCGAGGAGGGGAGAGCATCTATGGGAAGAAGAAGGGGCACTGAGGTTCCTCCTAGGGACCCCTAGATTTCACCAAGGCTAGTGCAGTTCCAGATGAACACGGACACCCTCCCCATGGGGATCCCAGTC Homo sapiens hg19 +JAK2_1.chr9.5073769.5073770_tile_1 JAK2_1.chr9.5073769.5073770_tile_1 1 chr9 5073737 5073923 + TATGTGTCTGTGGAGACGAGAGTAAGTAAAACTACAGGCTTTCTAATGCCTTTCTCAGAGCATCTGTTTTTGTTTATATAGAAAATTCAGTTTCAGGATCACAGCTAGGTGTCAGTGTAAACTATAATTT Homo sapiens hg19 +CDKN2A1.chr9.21971153.21971187_tile_1 CDKN2A1.chr9.21971153.21971187_tile_1 1 chr9 21971123 21971308 + GGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCC Homo sapiens hg19 +ABL1_1.chr9.133738330.133738364_tile_1 ABL1_1.chr9.133738330.133738364_tile_1 1 chr9 133738302 133738491 + CCATGAAGCACAAGCTGGGCGGGGGCCAGTACGGGGAGGTGTACGAGGGCGTGTGGAAGAAATACAGCCTGACGGTGGCCGTGAAGACCTTGAAGGTAGGCTGGGACTGCCGGGGGTGCCCAGGGTACGTGGGGCAAG Homo sapiens hg19 +ABL1_9.chr9.133747520.133747520_tile_1 ABL1_9.chr9.133747520.133747520_tile_1 1 chr9 133747476 133747664 + TTTCCTTCTGCAGGAGGACACCATGGAGGTGGAAGAGTTCTTGAAAGAAGCTGCAGTCATGAAAGAGATCAAACACCCTAACCTGGTGCAGCTCCTTGGTGAGTAAGCCCGGGGCTCTGAAGAGAGGGTCTCGCGCCGC Homo sapiens hg19 +ABL1_10.chr9.133748283.133748414_tile_1 ABL1_10.chr9.133748283.133748414_tile_1 1 chr9 133748157 133748327 - CCCGTAGGTCATGAACTCAGTGATGATATAGAACGGGGGCTCCCGGGTGCAGACCCCTGCCAACAAGACAACGAGGACTTCAACACGTGGCTCCGCTCCCAACTGAACAAACAACT Homo sapiens hg19 +ABL1_10.chr9.133748283.133748414_tile_2 ABL1_10.chr9.133748283.133748414_tile_2 1 chr9 133748277 133748457 + GAACCTCCTGGACTACCTGAGGGAGTGCAACCGGCAGGAGGTGAACGCCGTGGTGCTGCTGTACATGGCCACTCAGATCTCGTCAGCCATGGAGTACCTGGAGAAGAAAAACTTCATCCACAGGTAGGGGCCT Homo sapiens hg19 +ABL1_16.chr9.133750356.133750356_tile_1 ABL1_16.chr9.133750356.133750356_tile_1 1 chr9 133750328 133750516 + GCCCATGCTGGAGCCAAGTTCCCCATCAAATGGACTGCACCCGAGAGCCTGGCCTACAACAAGTTCTCCATCAAGTCCGACGTCTGGGGTAAGGGCTGCTGCTGCACTGAAGTGGTCCTTCCTGACTACAGGAGGGTT Homo sapiens hg19 +NOTCH1_1.chr9.139397768.139397768_tile_1 NOTCH1_1.chr9.139397768.139397768_tile_1 1 chr9 139397740 139397928 + CCAGGTAGACGATGGAGCTGGGCGGACAATCAGAGAGGGGCTGGGACCCGAGGCTTCCTCCTCCCCCGCCCACCGGCCAGGGATGCTGCCGCAGGACACTGAGGCCCATGACGCCACAGTCAGGACATGGTGAGGC Homo sapiens hg19 +NOTCH1_2.chr9.139399344.139399422_tile_1 NOTCH1_2.chr9.139399344.139399422_tile_1 1 chr9 139399316 139399485 + GCAGCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGCGCAGCTGCTCCGGCGGCATCAGCACCACCACCACCAGCGTGCCGGCCGCCAGCCTCTCGGGTACATGCTCCGC Homo sapiens hg19 +RET1.chr10.43609078.43609104_tile_1 RET1.chr10.43609078.43609104_tile_1 1 chr10 43609048 43609226 + CTGCTTCCCTGAGGAGGAGAAGTGCTTCTGCGAGCCCGAAGACATCCAGGGTGAGTGGGTGGCGGCCGGGACCACCACCACCTCCCAGCCCCACAGAGGTCTCAACAGCACATCTGAGGTCCCAACAA Homo sapiens hg19 +RET2_9.chr10.43609940.43609950_tile_1 RET2_9.chr10.43609940.43609950_tile_1 1 chr10 43609902 43610075 - TGGCTTGTGGGCAAACTTGTGGTAGCAGTGGATGCAGAAGGCAGACAGCAGCACCGAGACGATGAAGGAGAAGAGGACAGCGGCTGCGATCACCGTGCGGCACAGCTCGTCGCACAGTGG Homo sapiens hg19 +RET10.chr10.43613840.43613840_tile_1 RET10.chr10.43613840.43613840_tile_1 1 chr10 43613810 43613998 + CGAGTGAGCTGCGAGACCTGCTGTCAGAGTTCAACGTCCTGAAGCAGGTCAACCACCCACATGTCATCAAATTGTATGGGGCCTGCAGCCAGGATGGTAAGGCCAGCTGCAGGGTGAGGTGGGCAGCCACTGCACCCAG Homo sapiens hg19 +RET11_12.chr10.43615567.43615569_tile_1 RET11_12.chr10.43615567.43615569_tile_1 1 chr10 43615533 43615703 + CCTGGTAGCTGAGGGGCGGAAGATGAAGATTTCGGATTTCGGCTTGTCCCGAGATGTTTATGAAGAGGATTCCTACGTGAAGAGGAGCCAGGTGCCCAGTCCCGGGGATGAGGCGGGG Homo sapiens hg19 +RET13.chr10.43617416.43617416_tile_1 RET13.chr10.43617416.43617416_tile_1 1 chr10 43617388 43617564 + ATGGCAATTGAATCCCTTTTTGATCATATCTACACCACGCAAAGTGATGTGTAAGTGTGGGTGTTGCTCTCTTGGGGTGGAGGTTACAGAAACACCCTTATACATGTAGTGGGGCCACGACGC Homo sapiens hg19 +PTEN1.chr10.89624242.89624244_tile_1 PTEN1.chr10.89624242.89624244_tile_1 1 chr10 89624214 89624388 + CAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACCTTTCTGTCACTCTCTTAGAACGTGG Homo sapiens hg19 +PTEN3.chr10.89685307.89685307_tile_1 PTEN3.chr10.89685307.89685307_tile_1 1 chr10 89685275 89685459 + ATATACAATCTGTAAGTATGTTTTCTTATTTGTATGCTTGCAAATATCTTCTAAAACAACTATTAAGTGAAAGTTATCTGCTTGTTAGAGTGAGGTAGAGTTAAAGATACATTTTAACAGAATTGTATT Homo sapiens hg19 +PTEN4.chr10.89711893.89711900_tile_1 PTEN4.chr10.89711893.89711900_tile_1 1 chr10 89711865 89712039 + GTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN7.chr10.89717615.89717772_tile_1 1 chr10 89717489 89717668 + ATATTGCTGATATTAATCATTAAAATCGTTTTTGACAGTTTGACAGTTAAAGGCATTTCCTGTGAAATAATACTGGTATGTATTTAACCATGCAGATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_2 PTEN7.chr10.89717615.89717772_tile_2 1 chr10 89717615 89717801 - TTTAGCATCTTGTTCTGTTTGTGGAAGAACTCTACTTTGATATCACCACACACAGGTAACGGCTGAGGGAACTCAAAGTACATGAACTTGTCTTCCCGTCGTGTGGGTCCTGAATTGGAGGAATATATCTTCACC Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 1 chr10 89720684 89720870 + CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_2 PTEN13.chr10.89720716.89720852_tile_2 1 chr10 89720814 89720991 - TTCTTCATCAGCTGTACTCCTAGAATTAAACACACATCACATACATACAAGTCAACAACCCCCACAAAATGTTTAATTTAACTGACCTTAAAATTTGGAGAAAAGTATCGGTTGGCTTT Homo sapiens hg19 +FGFR2_1.chr10.123258034.123258034_tile_1 FGFR2_1.chr10.123258034.123258034_tile_1 1 chr10 123258006 123258184 + GATTTATGATATTCTTGTGTTTCCCAATCATCTTCATCATCTCCATCTCTGACACCAGATCAGAAAGGTCTTTCTCTGTGGCATCATCTATGAACAGTAGGCATATTCACAAATCAGTTCATTTC Homo sapiens hg19 +FGFR2_2.chr10.123274774.123274803_tile_1 FGFR2_2.chr10.123274774.123274803_tile_1 1 chr10 123274746 123274930 + CAGTAAATGGCTATCTCCAGGTAGTCTGGGGAAGCTGTAATCTCCTTTTCTCTTCCAGGCGCTAGATTGCAGATCACAGGAGGAGGAACAGATAAGCAGGCCATAGAGTTAGCACACCAGACTGACGCATC Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_1 FGFR2_5.chr10.123279503.123279677_tile_1 1 chr10 123279385 123279555 + AACAGGAAATCAAAGAACCTGTGGCCAAACCCATGAAGGAGACCCCAGTTGTGGGTACCTTTAGATTCAGAAAGTCCTCACCTTGAGAACCTTGAGGTAGGGCAGCCCGTCGGGCCC Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_2 FGFR2_5.chr10.123279503.123279677_tile_2 1 chr10 123279471 123279640 - ACGTAGAGTTTGTCTGCAAGGTTTACAGTGATGCCCAGCCCCACATCCAGTGGATCAAGCACGTGGAAAAGAACGGCAGTAAATACGGGCCCGACGGGCTGCCCTACCTCAAGGTT Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_3 FGFR2_5.chr10.123279503.123279677_tile_3 1 chr10 123279587 123279769 + TCTCCTCCGACCACTGTGGAGGCATTTGCCGGCAGTCCGGCTTGGAGGATGGGCCGGTGAGGCGATCGCTCTGGTGGAGAGAGGGAAGAAAGGAGGAGTGGGGATGGGAGAATGAGAGACCAATAAATA Homo sapiens hg19 +HRAS1.chr11.533873.533875_tile_1 HRAS1.chr11.533873.533875_tile_1 1 chr11 533843 534021 + CCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAATCCTGCAGGAGGACAGGGCTCAGGGACCCCCTCAGGACCTTCCGTGGGGGGA Homo sapiens hg19 +HRAS6.chr11.534285.534289_tile_1 HRAS6.chr11.534285.534289_tile_1 1 chr11 534251 534434 + GCCCACACCGCCGGCGCCCACCACCACCAGCTTATATTCCGTCATCGCTCCTCAGGGGCCTGCGGCCCGGGGTCCTCCTACAGGGTCTCCTGCCCCACCTGCCAAGGAGGGCCCTGCTCAGCCAGGCCCAGGC Homo sapiens hg19 +ATM1.chr11.108117847.108117848_tile_1 ATM1.chr11.108117847.108117848_tile_1 1 chr11 108117817 108117989 + TGTCACCAGGTACAGTAAGTAGGTCATGTCACATTTAGAAATTTCCTGTTAATTTTTTTTTTAAACTGGGCATTTTGGGCTTTTAAAACCTGTGTTCTCACAAAAAGCCTATAAAAT Homo sapiens hg19 +ATM2.chr11.108119823.108119823_tile_1 ATM2.chr11.108119823.108119823_tile_1 1 chr11 108119793 108119963 + TTGTGCCTTGGTAAAGTGTTACCATTTTCTCATTCAGTGTCATTTTAATCTCTTGTATGTTATTTTTCAGAAAACTTTCAGTGGAATCCTTTCATCTCAACCAGAACTAAGTCATTT Homo sapiens hg19 +ATM3.chr11.108123551.108123551_tile_1 ATM3.chr11.108123551.108123551_tile_1 1 chr11 108123513 108123683 + AGTAATTTTCCTCATCTTGTACTGGAGAAAATTCTTGTGAGTCTCACTATGAAAAACTGTAAAGCTGCAATGAATTTTTTCCAAAGCGTGCCAGAATGGTATGTTATCTAATA Homo sapiens hg19 +ATM4.chr11.108137973.108138003_tile_1 ATM4.chr11.108137973.108138003_tile_1 1 chr11 108137939 108138126 + TAATGGAGGTGGAGGATCAGTCATCCATGAATCTATTTAACGATTACCCTGATAGTAGTGTTAGTGATGCAAACGAACCTGGAGAGAGCCAAAGTACCATAGGTAAATACATATTTACTACTTGGGATT Homo sapiens hg19 +ATM6.chr11.108155132.108155132_tile_1 ATM6.chr11.108155132.108155132_tile_1 1 chr11 108155104 108155281 + GGCACAGCAAAGAGAGACTGCTACCAAGGTCTATGATATGCTTAAAAGTGAAAACTTATTGGGAAAACAGGTATGGCTTCAATTTTTATGTACTTTTCATTCCCTGAATGATATGAGATAT Homo sapiens hg19 +ATM7.chr11.108170476.108170479_tile_1 ATM7.chr11.108170476.108170479_tile_1 1 chr11 108170442 108170618 + GGGTCCTATAGATTTCTCTACCATAGCTATACAACATAGTAAAGATGCATCTTATACCAAGGCCCTTAAGTTATTTGAAGATAAAGAACTTCAGTGGACCTTCATAATGCTGACCTACCTGAA Homo sapiens hg19 +ATM9.chr11.108172421.108172421_tile_1 ATM9.chr11.108172421.108172421_tile_1 1 chr11 108172391 108172571 + TTAGCCACAAAGACTGGACATAGTTTCTGGGAGATTTATAAGATGACAACAGATCCAATGCTGGCCTATCTACAGCCTTTTAGAACATCAAGAAAAAAGGTCTCTTAAGTAATAAATGTTTATTGAA Homo sapiens hg19 +ATM10.chr11.108173640.108173640_tile_1 ATM10.chr11.108173640.108173640_tile_1 1 chr11 108173612 108173801 + AAATCTGTGGATTCCTCTAAGTGAAAATCATGACATTTGGATAAAGACACTGACTTGTGCTTTTTTGGACAGTGGAGGCACAAAATGTGAAATTCTTCAATTATTAAAGCCAATGTGTGAAGTAAGAAGATTAATT Homo sapiens hg19 +ATM11.chr11.108180945.108180945_tile_1 ATM11.chr11.108180945.108180945_tile_1 1 chr11 108180915 108181101 + AAGTTGCCAAGGTAGCTCAGTCTTGTGCTGCTCACTTTACAGCTTTACTCTATGCAGAAATCTATGCAGATAAGAAAAGTATGGATGATCAAGAGAAAAGGTAATGGAATTTAGAATTTTTGGTTTTTAAAA Homo sapiens hg19 +ATM12.chr11.108200958.108200961_tile_1 ATM12.chr11.108200958.108200961_tile_1 1 chr11 108200926 108201096 + TTCAGCGAGAGCTGGAGTTGGATGAATTAGCCCTGCGTGCACTGAAAGAGGATCGTAAACGCTTCTTATGTAAAGCAGTTGAAAATTATATCAACTGCTTATTAAGTGGAGAAGA Homo sapiens hg19 +ATM14.chr11.108204681.108204681_tile_1 ATM14.chr11.108204681.108204681_tile_1 1 chr11 108204651 108204823 + TACTATGGAAATTAAGGTAATTTGCAATTAACTCTTGATTTTTTTTAAACTAAATTTTTTTTATTAGATTGAACCATTTGAAATAGTATTTTTATGTAGGTCAAAATTGGTTAAATA Homo sapiens hg19 +ATM15.chr11.108205769.108205769_tile_1 ATM15.chr11.108205769.108205769_tile_1 1 chr11 108205739 108205928 + AGGTGTAAATTTACCAAAAATAATAGATTGTGTAGGTTCCGATGGCAAGGAGAGGAGACAGCTTGTTAAGGTGAGCCTTCCCTTCTCTGGCTTAGCCCTTAGAGTTTTAGTGATGAAAATTTTTAGTTCATATT Homo sapiens hg19 +ATM16.chr11.108206594.108206594_tile_1 ATM16.chr11.108206594.108206594_tile_1 1 chr11 108206566 108206750 + GATGCTGTCATGCAACAGGTCTTCCAGATGTGTAATACATTACTGCAGAGAAACACGGAAACTAGGAAGAGGAAATTAACTATCTGTACTTATAAGGTAACTATTTGTACTTCTGTTAGTTCACCAAAAAC Homo sapiens hg19 +ATM17.chr11.108218089.108218089_tile_1 ATM17.chr11.108218089.108218089_tile_1 1 chr11 108218061 108218247 + TCTAGGTAAGTAATAAAATCTATGTATCTATTCTTTTTAGTAAATATTTGGTCATCATGGAATGTTGTTTGCCTACCAAGATATTACAAATATAAGAGACAGATAAATTGAAGCAGTAAATATTGGGTTTTTT Homo sapiens hg19 +ATM18.chr11.108225590.108225590_tile_1 ATM18.chr11.108225590.108225590_tile_1 1 chr11 108225562 108225751 + AACCATTGTAGAGGTAAAGTATTTTATAAGGAAGACTTTATTTTTTTTCTTACCAGGTAGACTGTGTATCTCATCAGGAAGTCACTGATGTGAAGAGCACTGCTTCATTTTAACATAGGGGGATGTGGCTGGGCAGC Homo sapiens hg19 +ATM19.chr11.108236086.108236203_tile_1 ATM19.chr11.108236086.108236203_tile_1 1 chr11 108236058 108236241 + ACGTGTCTTAATGAGACTACAAGAGAAACTGAAAGGAGTGGAAGAAGGCACTGTGCTCAGTGTTGGTGGACAAGTGAATTTGCTCATACAGCAGGCCATAGACCCCAAAAATCTCAGCCGACTTTTCCCAG Homo sapiens hg19 +KRAS1.chr12.25378562.25378562_tile_1 KRAS1.chr12.25378562.25378562_tile_1 1 chr12 25378532 25378717 + TTGCTGATGTTTCAATAAAAGGAATTCCATAACTTCTTGCTAAGTCCTGAGCCTGTTTTGTGTCTACTGTTCTAGAAGGCAAATCACATTTATTTCCTACTAGGACCATAGGTACATCTTCAGAGTCCTTA Homo sapiens hg19 +KRAS2.chr12.25380275.25380283_tile_1 KRAS2.chr12.25380275.25380283_tile_1 1 chr12 25380245 25380427 + CCTCTTGACCTGCTGTGTCGAGAATATCCAAGAGACAGGTTTCTCCATCAATTACTACTTGCTTCCTGTAGGAATCCTGAGAAGGGAGAAACACAGTCTGGATTATTACAGTGCACCTTTTACTTCAA Homo sapiens hg19 +KRAS7.chr12.25398255.25398285_tile_1 KRAS7.chr12.25398255.25398285_tile_1 1 chr12 25398225 25398414 + TGTATCGTCAAGGCACTCTTGCCTACGCCACCAGCTCCAACTACCACAAGTTTATATTCAGTCATTTTCAGCAGGCCTTATAATAAAAATAATGAAAATGTGACTATATTAGAACATGTCACACATAAGGTTA Homo sapiens hg19 +PTPN11_1.chr12.112888163.112888211_tile_1 PTPN11_1.chr12.112888163.112888211_tile_1 1 chr12 112888135 112888323 + TGGTGATTACTATGACCTGTATGGAGGGGAGAAATTTGCCACTTTGGCTGAGTTGGTCCAGTATTACATGGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTCATTGAGCTTAAATATCCTCTGAACTGT Homo sapiens hg19 +PTPN11_10.chr12.112926884.112926888_tile_1 PTPN11_10.chr12.112926884.112926888_tile_1 1 chr12 112926856 112927032 + GGTCAGGGATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATATTGAAACACTACAGCGCAGGATTGAAGAAGAGCAGGTACCAGCCTGAGGGCTGGCATGCGG Homo sapiens hg19 +HNF1A_1.chr12.121431413.121431414_tile_1 HNF1A_1.chr12.121431413.121431414_tile_1 1 chr12 121431385 121431558 + GTGGGGCCCAGCATCCCAGCAGATCCTGTTCCAGGCCTATGAGAGGCAGAAGAACCCTAGCAAGGAGGAGCGAGAGACGCTAGTGGAGGAGTGCAATAGGTACAACGGCGGGCGGGAAACAG Homo sapiens hg19 +HNF1A_3.chr12.121432070.121432070_tile_1 HNF1A_3.chr12.121432070.121432070_tile_1 1 chr12 121432042 121432221 + GCGCAAAGAAGAAGCCTTCCGGCACAAGCTGGCCATGGACACGTACAGCGGGCCCCCCCCAGGGCCAGGCCCGGGACCTGCGCTGCCCGCTCACAGCTCCCCTGGCCTGCCTCCACCTGCCCTCTCCCCC Homo sapiens hg19 +FLT3_1.chr13.28592620.28592653_tile_1 FLT3_1.chr13.28592620.28592653_tile_1 1 chr13 28592590 28592766 + CATAGTTGGAATCACTCATGATATCTCGAGCCAATCCAAAGTCACATATCTTCACCACTTTCCCGTGGGTGACAAGCACGTTCCTGGCGGCCAGGTCTCTGTGAACACACTGTCAAGAATGA Homo sapiens hg19 +FLT3_13.chr13.28602329.28602329_tile_1 FLT3_13.chr13.28602329.28602329_tile_1 1 chr13 28602295 28602464 + GTGTGCACGCCCCCAGCAGGTTCACAATATTCTCGTGGCTTCCCAGCTGGGTCATCATCTTGAGTTCTGACATGAGTGCCTCTCTTTCAGAGCTGTCTGCTTTTTCTGTCAAAGAA Homo sapiens hg19 +FLT3_14.chr13.28608244.28608341_tile_1 FLT3_14.chr13.28608244.28608341_tile_1 1 chr13 28608214 28608402 + ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTAAATTGCTTCAGAGATGAAATGATGAGTCA Homo sapiens hg19 +FLT3_22.chr13.28610138.28610138_tile_1 FLT3_22.chr13.28610138.28610138_tile_1 1 chr13 28610098 28610267 - TATAGGAGTGAACCACTATGCCCAGCCAGTGAGCTTATTTCACACGTTCTTTTCTATAGGGAAACCTCAAGTGCTCGCAGAAGCATCGGCAAGTCAGGCGTCCTGTTTCTCGGATGG Homo sapiens hg19 +RB1_1.chr13.48919244.48919244_tile_1 RB1_1.chr13.48919244.48919244_tile_1 1 chr13 48919156 48919336 + ATTTACTTTTTTCTATTCTTTCCTTTGTAGTGTCCATAAATTCTTTAACTTACTAAAAGAAATTGATACCAGTACCAAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATGATGTATTG Homo sapiens hg19 +RB1_2.chr13.48923148.48923148_tile_1 RB1_2.chr13.48923148.48923148_tile_1 1 chr13 48923120 48923296 + TTATTAGCTAAAGGTAAGTTCATTATATTTATTAAATGCTAATATTTCAAATGTAATAATTAAATTGGCATTCCTTTGGACTAAATTCCCCAATTTTTATTGAGTAATGTACTCCTCCCTCAT Homo sapiens hg19 +RB1_3.chr13.48942685.48942685_tile_1 RB1_3.chr13.48942685.48942685_tile_1 1 chr13 48942655 48942826 + ACGAAAAAGTAACCTTGATGAAGAGGTGAATGTAATTCCTCCACACACTCCAGTTAGGTATGAATTTTCCTACTTTTAATTATATTATAATTTTGTTATTCATGGCTTTATAGTG Homo sapiens hg19 +RB1_4.chr13.48955538.48955550_tile_1 RB1_4.chr13.48955538.48955550_tile_1 1 chr13 48955504 48955684 + TAGAACGATGTGAACATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGAAATTCATTCATGTGCATATGGCTAACAAATTATTGTTAGTGAGAGGTGTTTCTTA Homo sapiens hg19 +RB1_6.chr13.49027168.49027168_tile_1 RB1_6.chr13.49027168.49027168_tile_1 1 chr13 49027112 49027288 + TTTGATCTTATTAAACAATCAAAGGACCGAGAAGGACCAACTGATCACCTTGAATCTGCTTGTCCTCTTAATCTTCCTCTCCAGAATAATCACACTGCAGCAGATATGTAAGCAAAATATA Homo sapiens hg19 +RB1_7.chr13.49033843.49033846_tile_1 RB1_7.chr13.49033843.49033846_tile_1 1 chr13 49033813 49033989 + TCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATGAGTATGAACTCATGAGAGACAGGCATTT Homo sapiens hg19 +RB1_8.chr13.49037877.49037877_tile_1 RB1_8.chr13.49037877.49037877_tile_1 1 chr13 49037815 49037985 + TTTACATCAATTTATTTACTAGATTATGATGTGTTCCATGTATGGCATATGCAAAGTGAAGAATATAGACCTTAAATTCAAAATCATTGTAACAGCATACAAGGATCTTCCTCA Homo sapiens hg19 +RB1_9.chr13.49039164.49039164_tile_1 RB1_9.chr13.49039164.49039164_tile_1 1 chr13 49039132 49039304 + AAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCCACCAGGGTAGGTCAAAAGTATCCTTTGATTGGAAAA Homo sapiens hg19 +AKT1.chr14.105246455.105246455_tile_1 AKT1.chr14.105246455.105246455_tile_1 1 chr14 105246429 105246600 + CTCACGTTGGTCCACATCCTGCGGCCGCTCCTTGTAGCCAATGAAGGTGCCATCATTCTTGAGGAGGAAGTAGCGTGGCCGCCAGGTCTTGATGTACTCCCCTACAGACGTGCGGGTGGTGA Homo sapiens hg19 +CDH1_1.chr16.68835649.68835650_tile_1 CDH1_1.chr16.68835649.68835650_tile_1 1 chr16 68835613 68835782 + TGGGCACAGATGGTGTGATTACAGTCAAAAGGCCTCTACGGTTTCATAACCCACAGATCCATTTCTTGGTCTACGCCTGGGACTCCACCTACAGAAAGTTTTCCACCAAAGTCACGCTGAAT Homo sapiens hg19 +CDH1_2.chr16.68846137.68846137_tile_1 CDH1_2.chr16.68846137.68846137_tile_1 1 chr16 68846109 68846283 + CGATAATCCTCCGATCTTCAATCCCACCACGGTAATTCTATAACTCCTTAGAGGGTTTCCAAAGAAAGGTCTTTTGTTGTTCATGAACTAAGTGTCACCACTGCTCATGGGCGAAGTCTTT Homo sapiens hg19 +CDH1_3.chr16.68847274.68847277_tile_1 CDH1_3.chr16.68847274.68847277_tile_1 1 chr16 68847246 68847422 + ACTGATGCTGATGCCCCCAATACCCCAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGAACAACGATGGCATTTTGAAAACAGCA Homo sapiens hg19 +TP53_1.chr17.7574003.7574021_tile_1 TP53_1.chr17.7574003.7574021_tile_1 1 chr17 7573977 7574147 + CGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATG Homo sapiens hg19 +TP53_3.chr17.7577022.7577129_tile_1 TP53_3.chr17.7577022.7577129_tile_1 1 chr17 7576996 7577166 + CGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCG Homo sapiens hg19 +TP53_17.chr17.7577523.7577574_tile_1 TP53_17.chr17.7577523.7577574_tile_1 1 chr17 7577495 7577683 + GGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGA Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_1 TP53_31_59.chr17.7578190.7578536_tile_1 1 chr17 7578064 7578234 + AGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTA Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_2 TP53_31_59.chr17.7578190.7578536_tile_2 1 chr17 7578156 7578325 - CTGATTGCTCTTAGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCC Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_3 TP53_31_59.chr17.7578190.7578536_tile_3 1 chr17 7578246 7578415 + TGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCG Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_4 TP53_31_59.chr17.7578190.7578536_tile_4 1 chr17 7578346 7578515 - GTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCG Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_5 TP53_31_59.chr17.7578190.7578536_tile_5 1 chr17 7578468 7578645 + CCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGA Homo sapiens hg19 +TP53_60.chr17.7579358.7579403_tile_1 TP53_60.chr17.7579358.7579403_tile_1 1 chr17 7579324 7579507 + GCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAG Homo sapiens hg19 +TP53_64.chr17.7579882.7579882_tile_1 TP53_64.chr17.7579882.7579882_tile_1 1 chr17 7579852 7580032 + GCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAG Homo sapiens hg19 +ERBB2_1.chr17.37880219.37880261_tile_1 ERBB2_1.chr17.37880219.37880261_tile_1 1 chr17 37880191 37880361 + TGTTGAGGGAAAACACATCCCCCAAAGCCAACAAAGAAATCTTAGACGTAAGCCCCTCCACCCTCTCCTGCTAGGAGGACAGGAAGGACCCCATGGCTGCAGGTCTGGGCTCTGGTCT Homo sapiens hg19 +ERBB2_4.chr17.37880993.37881012_tile_1 ERBB2_4.chr17.37880993.37881012_tile_1 1 chr17 37880963 37881151 + CGTGATGGCTGGTGTGGGCTCCCCATATGTCTCCCGCCTTCTGGGCATCTGCCTGACATCCACGGTGCAGCTGGTGACACAGCTTATGCCCTATGGCTGCCTCTTAGACCATGTCCGGGAAAACCGCGGACGCCTGGG Homo sapiens hg19 +ERBB2_13.chr17.37881332.37881440_tile_1 ERBB2_13.chr17.37881332.37881440_tile_1 1 chr17 37881298 37881482 + GCGGCTCGTACACAGGGACTTGGCCGCTCGGAACGTGCTGGTCAAGAGTCCCAACCATGTCAAAATTACAGACTTCGGGCTGGCTCGGCTGCTGGACATTGACGAGACAGAGTACCATGCAGATGGGGGCA Homo sapiens hg19 +SMAD4_1.chr18.48575169.48575170_tile_1 SMAD4_1.chr18.48575169.48575170_tile_1 1 chr18 48575131 48575301 + TTTGACTTAAAATGTGATAGTGTCTGTGTGAATCCATATCACTACGAACGAGTTGTATCACCTGGAATTGGTAAGTAGACTTTGCTTTCATCCTAAGAAACATAAAGGGAAA Homo sapiens hg19 +SMAD4_2.chr18.48581198.48581198_tile_1 SMAD4_2.chr18.48581198.48581198_tile_1 1 chr18 48581168 48581346 + AGGGACAGCCATCGTTGTCCACTGAAGGACATTCAATTCAAACCATCCAGCATCCACCAAGTAATCGTGCATCGACAGAGACATACAGCACCCCAGCTCTGTTAGCCCCATCTGAGTCTAATGC Homo sapiens hg19 +SMAD4_3.chr18.48584560.48584560_tile_1 SMAD4_3.chr18.48584560.48584560_tile_1 1 chr18 48584528 48584714 + GGGCCTCAGCCAGGACAGCAGCAGAATGGATTTACTGGTCAGCCAGCTACTTACCATCATAGTATGTACATACTTTAAAAAATCTTTTAAATAGTTGAGAAAAAAGTAGGCAGCCTTTATAAAAGCAAATTAAC Homo sapiens hg19 +SMAD4_4.chr18.48586262.48586262_tile_1 SMAD4_4.chr18.48586262.48586262_tile_1 1 chr18 48586234 48586416 + CCAGCCTCCCATTTCCAATCATCCTGGTAAGTGTATTTCAAAATTGATTTCCTGTATTTAGATTGATTTAGTGGTGATTGAAACGCACAAACACAGGCTTTAATGGAATTATGGGGTCACTTCTCAGAT Homo sapiens hg19 +SMAD4_5.chr18.48591826.48591919_tile_1 SMAD4_5.chr18.48591826.48591919_tile_1 1 chr18 48591796 48591982 + TTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAATGTCCACAGGAC Homo sapiens hg19 +SMAD4_11.chr18.48593405.48593405_tile_1 SMAD4_11.chr18.48593405.48593405_tile_1 1 chr18 48593377 48593547 + AAGGTGTGCAGTTGGAATGTAAAGGTGAAGGTGATGTTTGGGTCAGGTGCCTTAGTGACCACGCGGTCTTTGTACAGAGTTACTACTTAGACAGAGAAGCTGGGCGTGCACCTGGAGA Homo sapiens hg19 +SMAD4_12.chr18.48603032.48603094_tile_1 SMAD4_12.chr18.48603032.48603094_tile_1 1 chr18 48602998 48603168 + TGTCATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGCCCAGGATCAGTAGGTGGAATAGCTCCA Homo sapiens hg19 +SMAD4_15.chr18.48604668.48604754_tile_1 SMAD4_15.chr18.48604668.48604754_tile_1 1 chr18 48604638 48604808 + CGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTGGGGACCGGATTACCCAAGACAGAGCATCAAAGAAACACCTTGCTGGATTGAAATTCACTTACACCGGGCCCTCCAGC Homo sapiens hg19 +STK11_1.chr19.1207021.1207092_tile_1 STK11_1.chr19.1207021.1207092_tile_1 1 chr19 1206993 1207169 + CCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGTACCTGATGGGGGACCTGCTGGGGGAAGGCTCTTACGGCAAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGCAGGAGGGCCGT Homo sapiens hg19 +STK11_4.chr19.1220487.1220502_tile_1 STK11_4.chr19.1220487.1220502_tile_1 1 chr19 1220459 1220638 + CCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTTCGCGGCGGACGACACCTGCCG Homo sapiens hg19 +STK11_8.chr19.1221264.1221319_tile_1 STK11_8.chr19.1221264.1221319_tile_1 1 chr19 1221232 1221407 - CCCGCCTCCCTGGGGCTGCGGGCAGAGGGATGAGGCTCCCACCTTTCAGCAGGTCAGAGAGCGGGGGGCCACAGTCGCCCGGGATGGCGTAGCTCCCCTTCCCGATGTTCTCAAACAACTTG Homo sapiens hg19 +STK11_12.chr19.1223059.1223125_tile_1 STK11_12.chr19.1223059.1223125_tile_1 1 chr19 1223035 1223221 + GGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCC Homo sapiens hg19 +JAK3_1.chr19.17945696.17945696_tile_1 JAK3_1.chr19.17945696.17945696_tile_1 1 chr19 17945666 17945840 + GGTGACGCCACTAAACACTTCCCAGACCGTGGCGCCGAAGCCCCACTTGTCAGCTTCCAAGCTAAGTGTCTGCGCCTCCCGGAGACACTCGGGGGCCACCCAGGGGATCCTGTCGGTGAGCAC Homo sapiens hg19 +JAK3_2.chr19.17948009.17948009_tile_1 JAK3_2.chr19.17948009.17948009_tile_1 1 chr19 17947981 17948169 + CGCTGCTTCCAGGAATGACTGGGGAAGGTGGGAAGGGAGAGAAGATGCGTGGGTTTCTTCCACTCCAATAATCCCAAATTTTGTGCTCACAGACCTGCCTTAGGGGAACACCTGGCCACAGGTCACCTTTGGCCCTGG Homo sapiens hg19 +SRC.chr20.36031762.36031762_tile_1 SRC.chr20.36031762.36031762_tile_1 1 chr20 36031734 36031923 + CCAGCCCGGGGAGAACCTCTAGGCACAGGCGGGCCCAGACCGGCTTCTCGGCTTGGATCCTGGGCTGGGTGGCCCCTGTCTCGGGGCTTGCCCCACTCTGCCTGCCTGCTGTTGGTCCTCTCTCTGTGGGGCTGA Homo sapiens hg19 +GNAS1.chr20.57484420.57484421_tile_1 GNAS1.chr20.57484420.57484421_tile_1 1 chr20 57484390 57484560 + TGCCGTGTCCTGACTTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCAGTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCAC Homo sapiens hg19 +SMARCB1_1.chr22.24133967.24133990_tile_1 SMARCB1_1.chr22.24133967.24133990_tile_1 1 chr22 24133939 24134126 + TCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGGAGGCGACTAGCCACTGTGGAAGAGAGGAAGAAAATAGTTGCATCGTCACATGGTAAAAAAACAAAACCTAACACTAAGGGTGCGTCTTCACGAGGGTT Homo sapiens hg19 +SMARCB1_3.chr22.24143240.24143240_tile_1 SMARCB1_3.chr22.24143240.24143240_tile_1 1 chr22 24143210 24143383 + GGGCCGAGACAAGAAGAGAACCTTCCCCCTTTGGTGTGGATGCATCGCTGCACTCACCCTCCGTGCTGATTCCGCCTTAGTTCTCCAGCACGTTTCAGTTCCTTCCTCCCCAGAAAAACACT Homo sapiens hg19 +SMARCB1_4.chr22.24145582.24145582_tile_1 SMARCB1_4.chr22.24145582.24145582_tile_1 1 chr22 24145552 24145726 + GCTGCGAGACGCCTTCACCTGGAACATGAATGGTACAAGGCAGTCGGGCTTGGCTGGGCCTGGCCCCAACCCCTGTGTGTTACGTGGGAACAGTCCCGTTTCCTGCCAGCTGCCTGTCAGGC Homo sapiens hg19 +SMARCB1_5_6.chr22.24176352.24176357_tile_1 SMARCB1_5_6.chr22.24176352.24176357_tile_1 1 chr22 24176324 24176495 + CGGCCCCGGCCTGGTAACCAGCCCATCAGCACACGGCTCCCACGGAGCATCTCAGAAGATTGGGCCGCCTCTCCTCCATCTTCTGGCAAGGACAGAGGCGAGGGGACAGCCCAGCGCCA Homo sapiens hg19 +GNA11_4.chr19.3114942.3115070_tile_1 GNA11_4.chr19.3114942.3115070_tile_1 1 chr19 3114824 3115004 - GTAGCCCAAGGTGGCGATGCGGTCAACGTCGGTCAGGTAGCTGCAACACAGCGGTGGGTGCTCAGGCCGGCTGCCGGGGGTGGGGGGGCAGGACAGGGACACAGCACCCAAACCAGCGGGAGGACGGAAAGCCACC Homo sapiens hg19 +GNA11_4.chr19.3114942.3115070_tile_2 GNA11_4.chr19.3114942.3115070_tile_2 1 chr19 3114958 3115133 + CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCATCATCGAGTACCCTTTCGACCTGGAGAACATCATCTTCCGGTACCGCCCGGGCCACAGCAGGCGGGGAGGGGGCACTGAGA Homo sapiens hg19 +GNA11_5.chr19.3118922.3119051_tile_1 GNA11_5.chr19.3118922.3119051_tile_1 1 chr19 3118802 3118989 - CACTTCCTCCGCTCCGACCGCTGGCCCCCCACATCCACCATCCTGAAAGGACACAGCGCCAGGACTCAGCCACCTGGCGCCCCAAGGCCCAATCTGCAATCCCAGGACGGCTCCCACCCAAGCCCCTCCTGCCACACC Homo sapiens hg19 +GNA11_6.chr19.3119204.3119357_tile_2 GNA11_6.chr19.3119204.3119357_tile_2 1 chr19 3119208 3119395 - CCGCAGCCCGGCGCACCATCGAACTCGGGGAAGTAGTCCACCAGGTGCGAGTACAGGATCTTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGAGGATGACGGAGGAGTTCTGGAACCAGGGGTAGGTGATGATGGTCCGG Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_1 GNA11_7.chr19.3120987.3121177_tile_1 1 chr19 3120865 3121035 + GGGCCTTACTCGCTCATCCCCTGGGAGTGACAAAGGGGCCCACGAGTCCCTTGCCCTGGGCCGGGCTGGGGCACAGCCTCACCCTCTGCCCTCCCCCAGGTCCCCAGCGGGACGCCCAGGC Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 1 chr19 3120985 3121170 - CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTCCGTGTCGGTGGCACACGTGAAGTGTGAGTAGATGATCTTGTCGCTGTCGGGGTTCAGGTCCACGAACATCTTCAGGATGAACTCCCGCGCCGC Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_3 GNA11_7.chr19.3120987.3121177_tile_3 1 chr19 3121121 3121304 + GCAGCTCAACCTCAAGGAGTACAACCTGGTCTGAGCGCCCAGGCCCAGGGAGACGGGATGGAGACACGGGGCAGGACCTTCCTTCCACGGAGCCTGCGGCTGCCGGGCGGGTGGCGCTGCCGAGTCCGGGCCGGGGC Homo sapiens hg19 +GNAQ_4.chr9.80412436.80412564_tile_1 GNAQ_4.chr9.80412436.80412564_tile_1 1 chr9 80412406 80412592 + TACCTGAAAATGACACTTTGTAAGTCAAAGGGGTATTCGATGATCCCTGTGGTGGGGACTCGAACTCTAAGCACATCTTGTTGCGTAGGCAGGTAGGCAGGGTCAGCTACGCGGTCCAAGTCATTAAGATAGC Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_5.chr9.80409379.80409508_tile_1 1 chr9 80409249 80409421 + AAAGAAGTAAGTTCACTCCATTCCCCACACCCTACTTTCTATCATTTACTTGTATCAGATAATAAAATGATAATCCATTGCCTGTCTAAAGAACACTTACCTCATTGTCTGACT Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 1 chr9 80409335 80409510 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCAAGTTCTCGTGGAGTCAGACAATGAGGTAAGTGTTCTTTA Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_3 GNAQ_5.chr9.80409379.80409508_tile_3 1 chr9 80409459 80409639 + TTTGGCCCCCTACATCGACCATTCTGCAAGGTTAACAATACTCATATTAATAACATATAAAGTAAAACTAAAAAGTCAACATAAATATAGCACTACTTACAAACTTAGGGAAAATATTCTCTTGAAT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_6.chr9.80343430.80343583_tile_1 1 chr9 80343306 80343476 + GGGCAGCAATGGTGCACTGTAGTGCGTTAACTCCCACACTGGGGTTTGGAGACAAAACCTATTCACAGCTACTGAGCTGTGGTATGAGTGCTGACTTACCATCATATTCTGGGAAGT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_2 GNAQ_6.chr9.80343430.80343583_tile_2 1 chr9 80343392 80343561 - GGTTCCAGAACTCCTCGGTTATTCTGTTCTTAAACAAGAAAGATCTTCTAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGTAAGTCAGCAC Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_3 GNAQ_6.chr9.80343430.80343583_tile_3 1 chr9 80343504 80343689 + CAGGGGTATGTGATAATTGTTCTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTGGAAAAAAAAAAAAAATCAGAAAAAACAAGGAGTGAATTACATGATTACTTAATTTGTGAATTGTGTTTATTTT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 1 chr9 80336110 80336280 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCAGGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAATTAGACCAGATTGTACT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_7.chr9.80336240.80336429_tile_2 1 chr9 80336204 80336374 - CTACTCCCACTTCACGTGCGCCACAGACACCGAGAATATCCGCTTTGTCTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGAGTACAATCTGGTCTAATTGTGCCTCC Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_3 GNAQ_7.chr9.80336240.80336429_tile_3 1 chr9 80336320 80336495 + GATAATTTTGTCACTGTCTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCTTTCGGCCAAGAGACAAGAGGGACACTTTGTTACCTA Homo sapiens hg19 +PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 2 chr22 17052964 17053133 + ATCCTCTCTCTGAAATCACTGCGCAGGAGAAAGATTTTCTATGGACCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGACTTTGG Homo sapiens hg19 +PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 2 chr22 17055413 17055585 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTGTCAAACAGGAGAAGAAGGATGAAACACAAAAGTTGTGTGACTCTAGTCTGTGTTTGAGACTCTT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN3.chr10.89685307.89685307_tile_1 2 chr9 33675957 33676480 - ATACACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATCTAATTACAGAGTTGCGCAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTATAATGATTTATGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 2 chr9 33675629 33675815 - CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAGTATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 +GNA11_6.chr19.3119204.3119357_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 2 chr7 65970150 65970483 + CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTTCGTGTCGGTGGCGTACGTGAAGTGGGAGTCGATGATCTTGTCGCTGTCGGGGTTCATGTCCACTAACATCTTCAGGATGAACTCCCGCGCCGCCTGGGCGTCCTGCTGGGGCCCTTCGAACTCGGGGAAGTAGTCCACCATGTGTGAGTACAGGATATTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGGTGATGACGGGGGAGTTCTGGAACCAGGGGTAGTCGATGATGGTCCGG Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_1 GNA11_4.chr19.3114942.3115070_tile_2 2 chr7 65970285 65970719 - CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCGTCTTTCGACCTGGAGAACATCATCTTCAGGATGGCGGATGTTGGGGGACAGCGGTCGGCGCAGAGGAAGTGGATCCACTGCTTTGAGAACCTGACGTCCATCCCGTTTCTCGTCGCCCTCAGTGAATACGACCAAGTCCTGGTGGAGTCGGACAACGAGAACCGGATGGAGGAGAGCAAAGCCCTGTTCCGGACCATCATCGACTACCCCTGGTTCCAGAACTCCCCCGTCATCACCTTCCTCAACAAGAAGGACCTGCTGGAGGACAATATCCTGTACTCACACATGGTGGACTACTTCCCCGAGTTCGAAGGGCCCCAGCAGGACGCCCAGGC Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 2 chr2 132181238 132181750 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCATGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAACTAGACCAGATTGTAATCCTTCAGGTTCAACTGGAGGATGGTGTCCTTGACGGCAGCAAACACAAAGCGGATATTCTCGGTGTCTGTGGCGCATGTGAAGTGGGAGTAGATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGTAGTCGACTAGATGGGAATACATGATTTTCTCCTCTGGAAGATCTTTCTTGTTTAACAACAGAATAACCGAGGAGTTCTGGAACCAGGGATACGTGATAATTGTACTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTCATTGTCTGACT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_7.chr9.80336240.80336429_tile_3 2 chr2 132181448 132181600 + GATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 2 chr2 132181332 132181839 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCGAGTTCTCGTGGAGTCAGACAATGAGAACCGAATGGAGGAAAGCAAGGCTCTCTTTAGTACAATTATCACGTATCCCTGGTTCCAGAACTCCTCGGTTATTCTGTTGTTAAACAAGAAAGATCTTCCAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGACCCCAGAGAGATGCCCAGGCAGCCCGAGAATTCATTCTGAAGATGTTCGTGGACCTGAACCCAGTGACCAAATTATCTACTCCCACTTCACATGCGCCACAGACACCGAGAATATCCGCTTTGTGTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGATTACAATCTGGTCTAGTTGTGCCTCC Homo sapiens hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/TSACP/TruSeq_Custom_Amplicon_Control_Manifest_ACP1.txt Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,695 @@ +[Header] +Customer Name Illumina +Product Type 15025138 +Date Manufactured +Lot +DesignStudio ID TSCA_Control +Target Plexity 341 + +[Probes] +Target Region Name Target Region ID Target ID Species Build ID Chromosome Start Position End Position Submitted Target Region Strand ULSO Sequence ULSO Genomic Hits DLSO Sequence DLSO Genomic Hits Probe Strand Designer Design Score Expected Amplifed Region Size SNP Masking Labels +snp_rs10138962 snp_rs10138962 snp_rs10138962 Homo sapiens hg19 chr14 104995819 104995868 + AAGCCAAGAACCCTCTCAGGCT 282 TGCGCACCTGTGGTCCCAGCTACTCA 1200 + ILLUMINA 5.13E-61 191 FALSE ACP1 +snp_rs1149580 snp_rs1149580 snp_rs1149580 Homo sapiens hg19 chr11 76549431 76549489 + GGATCAATGAACAGGTTATACAGGCTG 32 ACTGGGGACAAAGGGATAAACTAGACC 68 + ILLUMINA 0.817486141 200 FALSE ACP1 +snp_rs10988298 snp_rs10988298 snp_rs10988298 Homo sapiens hg19 chr9 132042416 132042471 + GAGGCTGAGATGGGAGGATCACTTGAA 1200 ATTGTGCACCCTCCATACAAATGTATG 75 + ILLUMINA 2.84E-58 197 FALSE ACP1 +snp_rs10086550 snp_rs10086550 snp_rs10086550 Homo sapiens hg19 chr8 143362946 143363004 + GTGTGACTACAGTGGGAAGAGGACAT 51 CATAGAGGAAGGGCTGTGGCCCA 73 + ILLUMINA 0.38673505 200 FALSE ACP1 +snp_rs10409978 snp_rs10409978 snp_rs10409978 Homo sapiens hg19 chr19 57796594 57796646 + TGTCTTACTTAGAAAGGGTTGGCTACG 50 TTATGGGTCTGCTCCTGTCACTGTCTT 115 + ILLUMINA 0.584760563 194 FALSE ACP1 +snp_rs1060493 snp_rs1060493 snp_rs1060493 Homo sapiens hg19 chr15 31516370 31516476 + AAACCCTCTGCTGGGACCGCCAA 23 TGAGGAGCCGTGGGGCTCACGTTTCA 12 + ILLUMINA 0.070951385 248 FALSE ACP1 +snp_rs12777222 snp_rs12777222 snp_rs12777222 Homo sapiens hg19 chr10 35387873 35387930 + TAGTGAGTTGAGATTGCATCATTGCAC 1163 GAACAAATGGACTAAAAGACGTAGTTCC 47 + ILLUMINA 1.21E-54 199 FALSE ACP1 +snp_rs12563211 snp_rs12563211 snp_rs12563211 Homo sapiens hg19 chr1 34486119 34486219 + TCAGGCAGCAACAACGCCCTGAGCAA 19 AAATTGTGCATGACCTTTAGGTCCTGG 47 + ILLUMINA 0.272884262 242 FALSE ACP1 +snp_rs10843013 snp_rs10843013 snp_rs10843013 Homo sapiens hg19 chr12 28025101 28025174 + ACTAATCCTACCCTTAAGGCTTTCTTT 41 ATCACAGCTCCATATATGCCTTGTGTG 47 + ILLUMINA 0.646311699 215 FALSE ACP1 +snp_rs12678837 snp_rs12678837 snp_rs12678837 Homo sapiens hg19 chr8 22950305 22950356 + GCAGTCCAGCTCTGATGGAGCTGTCA 53 TGCATCCTCATCAGTGGGCCCAGGTT 46 + ILLUMINA 0.608241088 193 FALSE ACP1 +snp_rs10954737 snp_rs10954737 snp_rs10954737 Homo sapiens hg19 chr7 83532935 83533038 + GAGGCAGCTTGTAAGTTATAAGAAATC 35 AAAACTGTTTTGAAGGGCTCAAGCCC 66 + ILLUMINA 0.265474762 245 FALSE ACP1 +snp_rs11100509 snp_rs11100509 snp_rs11100509 Homo sapiens hg19 chr4 164478785 164478875 + CACATTCTAGAACAGTTCCCATTTTTC 105 AAATCTTCATGTTGAATACTTTTTCACTG 261 + ILLUMINA 0.002100139 232 FALSE ACP1 +snp_rs12636227 snp_rs12636227 snp_rs12636227 Homo sapiens hg19 chr3 65065386 65065482 + CATTTGTGGAAGCAAGGCATCCTTCT 53 AAAACCACAGGACTTAGGGCAAAATGG 61 + ILLUMINA 0.398397766 238 FALSE ACP1 +snp_rs10038337 snp_rs10038337 snp_rs10038337 Homo sapiens hg19 chr5 11512340 11512425 + CAACACAGTGTTTGCTTTAATGCTCTG 165 ATCTAGGCAGTTAGGATGTCCATTAAC 49 + ILLUMINA 0.091055737 227 FALSE ACP1 +snp_rs10509415 snp_rs10509415 snp_rs10509415 Homo sapiens hg19 chr10 82472980 82473063 + AATAGTGGGGAAATCATCTTGCCTCAG 59 TCTATGGATTTATAGAGGAGTAGAAGAGG 166 + ILLUMINA 0.114550875 225 FALSE ACP1 +snp_rs10757399 snp_rs10757399 snp_rs10757399 Homo sapiens hg19 chr9 23186370 23186421 + GCCATCGTACAGCTAAATTTGTAAGTGG 28 TGGGAGTTTTGAACATATTTTAGGCAA 240 + ILLUMINA 0.01822009 193 FALSE ACP1 +snp_rs10919337 snp_rs10919337 snp_rs10919337 Homo sapiens hg19 chr1 170216910 170216970 + GAAGCATTTAATGAAATAAAGCAGAGAAG 533 TTTAAAGGAAGCTGCCCAGAACTGC 91 + ILLUMINA 3.17E-11 202 FALSE ACP1 +snp_rs11205541 snp_rs11205541 snp_rs11205541 Homo sapiens hg19 chr1 49254315 49254404 + GTGAAACACAGTGTTCTCAATCATAAA 68 TTTACTATTGAACTATTTGGTGAGCGC 56 + ILLUMINA 0.366528454 231 FALSE ACP1 +snp_rs10819072 snp_rs10819072 snp_rs10819072 Homo sapiens hg19 chr9 101361505 101361553 + TCCAACCTAGGGGCTTCAAACTCAGTT 38 GGAAGGTTCTGTAGACAAGCAGAACA 52 + ILLUMINA 0.905035471 190 FALSE ACP1 +snp_rs1078814 snp_rs1078814 snp_rs1078814 Homo sapiens hg19 chr3 193732947 193733001 + TTTATGCCGATTTTACTGGCCTCGTTG 17 GATAGCTCCCATGGATGGTGAGTGAAA 76 + ILLUMINA 0.746851007 196 FALSE ACP1 +snp_rs10487657 snp_rs10487657 snp_rs10487657 Homo sapiens hg19 chr7 82713031 82713144 + TGGTAAATGAGTCTGTTTCCTATTAGTG 74 ACATTTAATTCTCATTTGGCATTTGTAAG 210 + ILLUMINA 0.009085148 255 FALSE ACP1 +snp_rs10930331 snp_rs10930331 snp_rs10930331 Homo sapiens hg19 chr2 151750556 151750607 + GTAGTATGACTTAAGTGAGAGAGGAAG 54 CTGCATTATTAGCTATACAGCAAACAG 69 + ILLUMINA 0.755023344 193 FALSE ACP1 +snp_rs11075329 snp_rs11075329 snp_rs11075329 Homo sapiens hg19 chr16 17123751 17123840 + CTCAGTGGTTTGGCATAATGGAAATTC 56 AAGAAGGAGCTGGCATTCAAGTCTTG 100 + ILLUMINA 0.363982947 231 FALSE ACP1 +snp_rs10050438 snp_rs10050438 snp_rs10050438 Homo sapiens hg19 chr5 10139056 10139128 + TAGGAGGATCTGCCTGACCCAAATGA 43 AGGTGATCCGGCACCCGCAAATTCAGA 36 + ILLUMINA 0.590150376 214 FALSE ACP1 +snp_rs10425564 snp_rs10425564 snp_rs10425564 Homo sapiens hg19 chr19 57312898 57312973 + GTGCGGAAATAGAGATGTTTGCTGTAC 43 AAAATACCTCTGCTCTCAAAAGGGCA 84 + ILLUMINA 0.502413289 217 FALSE ACP1 +snp_rs11266838 snp_rs11266838 snp_rs11266838 Homo sapiens hg19 chr7 126792754 126792832 + AAGGTCAGCCTAGTGTCCTTAGGTGA 27 TTTCAGACATGTTTCATAGGACTACAG 51 + ILLUMINA 0.449172653 220 FALSE ACP1 +snp_rs10870311 snp_rs10870311 snp_rs10870311 Homo sapiens hg19 chr10 134290435 134290493 + ATTAATCAGCCCAACCTTTGCATCTGC 49 TTGCAGGACTCATGGTGCAGGGT 45 + ILLUMINA 0.503025892 200 FALSE ACP1 +snp_rs10993058 snp_rs10993058 snp_rs10993058 Homo sapiens hg19 chr9 96873061 96873137 + TAACCTGGCAAAGCTGCCCGTCAAAGT 52 AGGAAGTACATGATTTCTTGCCACTGT 76 + ILLUMINA 0.580524574 218 FALSE ACP1 +snp_rs10972175 snp_rs10972175 snp_rs10972175 Homo sapiens hg19 chr9 34625323 34625384 + GCTCTGACATTCCTGGAAAGGAATTTC 99 GACCCTGGACACAGAACCAAGGCATT 92 + ILLUMINA 0.510432046 203 FALSE ACP1 +snp_rs11582151 snp_rs11582151 snp_rs11582151 Homo sapiens hg19 chr1 37796519 37796576 + GCAAGATGGGTCACCAGCAGCTCTACT 60 AGTAGATTAGCCAAGGCACCCACTCAA 30 + ILLUMINA 0.745283701 199 FALSE ACP1 +snp_rs11085825 snp_rs11085825 snp_rs11085825 Homo sapiens hg19 chr19 13007357 13007445 + CTTTGTCAGGCAGGCTCCGTGCT 47 TCAGCCTCCTGGCTCTGAGCATCGAA 71 + ILLUMINA 0.187309361 230 FALSE ACP1 +snp_rs10246620 snp_rs10246620 snp_rs10246620 Homo sapiens hg19 chr7 43424032 43424089 + AGCCCCAGGAACACCTCTGGAGGGAAT 74 AAAAATACGTCTTTGCCTAAAACTTAAAC 94 + ILLUMINA 0.32864177 199 FALSE ACP1 +snp_rs11045044 snp_rs11045044 snp_rs11045044 Homo sapiens hg19 chr12 20257796 20257887 + TGAAAACCCATCCATTGACCCATTTATC 77 CACTCTCATTCGTATACTTTAGACTTGTG 39 + ILLUMINA 0.314654098 233 FALSE ACP1 +snp_rs10189240 snp_rs10189240 snp_rs10189240 Homo sapiens hg19 chr2 144484408 144484483 + ACCTAACCAAGTATCTGTACCTCCACA 37 ATAAATCTCAGCTTGGGATCCACAGAC 82 + ILLUMINA 0.583256128 217 FALSE ACP1 +snp_rs11008285 snp_rs11008285 snp_rs11008285 Homo sapiens hg19 chr10 31130903 31130970 + ACTCCAGCCTGGATGACAGAGCAAGA 1200 TTCTCCCAAGTCTGGCCAAAAGCCTAA 67 + ILLUMINA 2.40E-58 209 FALSE ACP1 +snp_rs11139732 snp_rs11139732 snp_rs11139732 Homo sapiens hg19 chr9 85365424 85365500 + TCTGATGGAGATCTTATTCTCCCAGAG 54 AATCTGGAGTCCATTTTGCCCATGCA 44 + ILLUMINA 0.55328873 218 FALSE ACP1 +snp_rs10736719 snp_rs10736719 snp_rs10736719 Homo sapiens hg19 chr11 61999654 61999714 + CTTAGAAGCCCAAATTAAGTTCAGAAAC 70 CTCTGAATGAGGATTTGGTTCATAGGG 44 + ILLUMINA 0.669444255 202 FALSE ACP1 +snp_rs10891556 snp_rs10891556 snp_rs10891556 Homo sapiens hg19 chr11 113352679 113352753 + TGTTCCACACTGCAAAACAATGCTGC 57 ATCAATGAGGTTTGGAAAGGGTGGCA 84 + ILLUMINA 0.510725191 216 FALSE ACP1 +snp_rs10741165 snp_rs10741165 snp_rs10741165 Homo sapiens hg19 chr10 130610943 130611010 + TGAAATTCAACAATTTCCTTCGAAAGC 110 ATCCTGAGAATAATAGTAAGAGCGGCC 43 + ILLUMINA 0.412482229 209 FALSE ACP1 +snp_rs1055273 snp_rs1055273 snp_rs1055273 Homo sapiens hg19 chr16 58028857 58028938 + AAGAATTAGCAGTTGGGACGGTTGTAG 27 TCAGGGCCCTTGGTGTGCCCACTGATTA 50 + ILLUMINA 0.469236873 223 FALSE ACP1 +snp_rs10740396 snp_rs10740396 snp_rs10740396 Homo sapiens hg19 chr10 74019951 74020035 + GATCCTGTTCCATGTGGCAAGAGCTT 55 AAGAGGCAAATAGGTATGTAGGTCAGC 53 + ILLUMINA 0.545209534 226 FALSE ACP1 +snp_rs10112900 snp_rs10112900 snp_rs10112900 Homo sapiens hg19 chr8 19646421 19646483 + GATGACTGTATTTGGAAGGTAGTTCAG 53 TAATCTCCCTGAAAACGGACCATTACA 47 + ILLUMINA 0.75040328 204 FALSE ACP1 +snp_rs10422772 snp_rs10422772 snp_rs10422772 Homo sapiens hg19 chr19 9723318 9723425 + AACTCTTCACAAAACCCCACTGCCT 71 TTATTATTATGCAGGGTGGTTTGAGAC 66 + ILLUMINA 0.202458701 249 FALSE ACP1 +snp_rs11002468 snp_rs11002468 snp_rs11002468 Homo sapiens hg19 chr10 80011963 80012029 + TCTCCAAGCATGGCTCCCATCTGGTTA 57 TGTGCCCATAGGCACCTCCTGGGAAT 59 + ILLUMINA 0.642689469 208 FALSE ACP1 +snp_rs11044070 snp_rs11044070 snp_rs11044070 Homo sapiens hg19 chr12 18546143 18546219 + CATGGTAACTCCCTTTAAATATCAGAGG 61 ATAGATGGAGAACAGCCTTCAATGTGG 67 + ILLUMINA 0.613806499 218 FALSE ACP1 +snp_rs10139797 snp_rs10139797 snp_rs10139797 Homo sapiens hg19 chr14 101708517 101708578 + AGATCCTGACCATGGAAGAATCAGAGG 59 GATGACCCAGTGAATGCGGGGCACA 27 + ILLUMINA 0.570836291 203 FALSE ACP1 +snp_rs10825371 snp_rs10825371 snp_rs10825371 Homo sapiens hg19 chr10 56435269 56435346 + AATTCTAAGGCCTTTTCATGTTGTTTT 120 ACTTCCTCCCCCAAGTATAGGTCAAA 38 + ILLUMINA 0.216134472 219 FALSE ACP1 +snp_rs11017755 snp_rs11017755 snp_rs11017755 Homo sapiens hg19 chr10 132944089 132944152 + CCTTGTAGCCAGGCATCTCTGCCTCT 54 GTTCCTCTCTGTTTCTTGGCGAAACA 54 + ILLUMINA 0.62682178 205 FALSE ACP1 +snp_rs11134290 snp_rs11134290 snp_rs11134290 Homo sapiens hg19 chr5 8202447 8202503 + ATGATGATACTCAGCCCAAGGGAGCT 39 CAAATCCCATTAGGGGCTTTGGACAT 42 + ILLUMINA 0.78115378 198 FALSE ACP1 +snp_rs10803015 snp_rs10803015 snp_rs10803015 Homo sapiens hg19 chr1 242243096 242243148 + CTGACCTCTGGTGATCCACCTGCCTA 1200 GGCAATGAGAGTTGTCCTCTCTGTGT 65 + ILLUMINA 2.63E-58 194 FALSE ACP1 +snp_rs1038074 snp_rs1038074 snp_rs1038074 Homo sapiens hg19 chr5 150358860 150358935 + AAGCGCGCAGTTATGTTTCTATAGAAA 58 GATATGAATGTTACTATATGTGCCACTAC 61 + ILLUMINA 0.485826376 217 FALSE ACP1 +snp_rs10207380 snp_rs10207380 snp_rs10207380 Homo sapiens hg19 chr2 241860797 241860881 + CATTGTTGCTGGCACCCCTGGGA 23 CACAGAAATGCTGCCGACAGATTAGT 28 + ILLUMINA 0.159512362 226 FALSE ACP1 +snp_rs10235210 snp_rs10235210 snp_rs10235210 Homo sapiens hg19 chr7 116003359 116003415 + ACTCTTTATGGGCAAAAATTTATTCTTTC 196 ATATGCTCTTCACAGGAGTTTCCACTC 66 + ILLUMINA 0.062074325 198 FALSE ACP1 +snp_rs10185490 snp_rs10185490 snp_rs10185490 Homo sapiens hg19 chr2 71166760 71166812 + GGAGGTAGGGGCGGCAGTGTACAAACAA 44 ATCCCTCTAGGGTCCCAGTCTGTAGTA 39 + ILLUMINA 0.731156187 194 FALSE ACP1 +snp_rs10109406 snp_rs10109406 snp_rs10109406 Homo sapiens hg19 chr8 72632603 72632656 + GCACTGGCTATATCTCCACTCCTTTCT 35 TACAGATGCCCCCATGGTGGGATCTTA 31 + ILLUMINA 0.833771305 195 FALSE ACP1 +snp_rs10095650 snp_rs10095650 snp_rs10095650 Homo sapiens hg19 chr8 82918286 82918381 + GAATCCATATTAAATGACAGTATCCTGTC 89 TTCTCCTGAGAGGTGACTGTGATATCG 56 + ILLUMINA 0.299972573 237 FALSE ACP1 +snp_rs10840020 snp_rs10840020 snp_rs10840020 Homo sapiens hg19 chr11 8339791 8339873 + AATGGCCTACAGTTGCCAAATTTTGT 50 AAACCTCATTCCCAGAGGGTCAAGCAT 63 + ILLUMINA 0.502325149 224 FALSE ACP1 +snp_rs10502584 snp_rs10502584 snp_rs10502584 Homo sapiens hg19 chr18 29797390 29797460 + GAAAAAGTCCTCATAACAGTCCAGTCA 43 TGTTTTAGTATCAGATTAGGAGGAATTCC 69 + ILLUMINA 0.547938278 212 FALSE ACP1 +snp_rs10106093 snp_rs10106093 snp_rs10106093 Homo sapiens hg19 chr8 29355343 29355403 + GGAGGAGAGACAGCATCTCCTCTGT 68 GAGAATTAAGCTCTGTGGTCAGACTCT 60 + ILLUMINA 0.681295961 202 FALSE ACP1 +snp_rs10832136 snp_rs10832136 snp_rs10832136 Homo sapiens hg19 chr11 13925649 13925709 + TTAATGTGACTACTAGAGTGGCATACGC 44 TTGTCGTCTTTGGTAGTGGGCATGGAA 60 + ILLUMINA 0.81035586 202 FALSE ACP1 +snp_rs1028530 snp_rs1028530 snp_rs1028530 Homo sapiens hg19 chr14 27441076 27441125 + TCATTGCAATAGAATATTAATAGGCGATG 140 TGTGCACGATGGCACCAATGAATA 43 + ILLUMINA 0.211021279 191 FALSE ACP1 +snp_rs10936922 snp_rs10936922 snp_rs10936922 Homo sapiens hg19 chr3 176675194 176675287 + GGGACTCTTCCAGATGCATTCTGAGTT 60 TAATTGTTGTTTTCCTAAGACGGAGTC 162 + ILLUMINA 0.104925708 235 FALSE ACP1 +snp_rs10184938 snp_rs10184938 snp_rs10184938 Homo sapiens hg19 chr2 9912919 9912986 + CTGTTCCCACAAGACTCGGGTGGTT 20 TCCATCTTTCAAAGACAGGCCTTAGAG 71 + ILLUMINA 0.553442177 209 FALSE ACP1 +snp_rs1028850 snp_rs1028850 snp_rs1028850 Homo sapiens hg19 chr13 40941401 40941454 + GGAATCTTAATCAGAACCTCAAAGCAC 53 GAGAATGGAAACAACCCACTCTATCCT 38 + ILLUMINA 0.842123958 195 FALSE ACP1 +snp_rs10913469 snp_rs10913469 snp_rs10913469 Homo sapiens hg19 chr1 177913436 177913498 + GAAAGGGAGAGCTGTCTGGAGAGAT 68 AAGAAATCCTACACCCTCCCACGCTTA 36 + ILLUMINA 0.683245768 204 FALSE ACP1 +snp_rs10490198 snp_rs10490198 snp_rs10490198 Homo sapiens hg19 chr2 67121590 67121670 + CCTGTCCTCCTCAAGTTAAGACAACCA 56 ATTGCTGCTCATGGTTACATGGTGAAC 62 + ILLUMINA 0.522152761 222 FALSE ACP1 +snp_rs1147960 snp_rs1147960 snp_rs1147960 Homo sapiens hg19 chr10 44971382 44971462 + CTGTGTCTAACATAGTTGTAACATGTC 31 ATGAATGGACAGAGCCATGTGACCA 87 + ILLUMINA 0.340999248 222 FALSE ACP1 +snp_rs10489168 snp_rs10489168 snp_rs10489168 Homo sapiens hg19 chr1 44727899 44727972 + GAAGTGTGACAAGGACAATAACCCCCA 39 ACTCCCTCTCTGGAAATCCAGCAGTT 76 + ILLUMINA 0.575405881 215 FALSE ACP1 +snp_rs11241298 snp_rs11241298 snp_rs11241298 Homo sapiens hg19 chr5 114282959 114283018 + TGCATCCACAACACATGAATTGAGGAC 61 AAAGAGAAGGGATGGGGATCGAGAAA 59 + ILLUMINA 0.818091155 201 FALSE ACP1 +snp_rs10935172 snp_rs10935172 snp_rs10935172 Homo sapiens hg19 chr3 135275607 135275671 + CTCCCACAGAAGCAGCATGCAGTCA 72 AGACTCACAGACAAGACTGTGAAGCT 60 + ILLUMINA 0.596164301 206 FALSE ACP1 +snp_rs10746385 snp_rs10746385 snp_rs10746385 Homo sapiens hg19 chr1 219706324 219706397 + GACAGAATCAGACCTATAAGGTTTCTC 48 TACAGTATGCCATCAAGCCCCCTTCAT 34 + ILLUMINA 0.567502432 215 FALSE ACP1 +snp_rs10834253 snp_rs10834253 snp_rs10834253 Homo sapiens hg19 chr11 24001879 24001968 + GCTCAATGCACTGATTTAAGTCATAAG 52 AGGAAAGTAGCAAATTATCCTCACACA 79 + ILLUMINA 0.391011516 231 FALSE ACP1 +snp_rs10068395 snp_rs10068395 snp_rs10068395 Homo sapiens hg19 chr5 178252283 178252356 + CGTCTAGTGGCTCACATGAATATTTCTG 60 TCCTCTCGGGTTCCTCCCCAGATATTA 63 + ILLUMINA 0.625549047 215 FALSE ACP1 +snp_rs10482536 snp_rs10482536 snp_rs10482536 Homo sapiens hg19 chrX 123884103 123884173 + AACAGTAGACCAAGATGGGGAGAGGTA 53 CCAAATGAAATAAGTGACCTACAAAGT 95 + ILLUMINA 0.453117563 212 FALSE ACP1 +snp_rs10512096 snp_rs10512096 snp_rs10512096 Homo sapiens hg19 chr9 82730243 82730336 + CCGATAAGAACTTTTGTGCCTCCTTC 40 ACATCATATTAGGTTCTGATTACAGATGC 72 + ILLUMINA 0.292524473 235 FALSE ACP1 +snp_rs10765017 snp_rs10765017 snp_rs10765017 Homo sapiens hg19 chr10 129168799 129168867 + TCTGGCAAGTGCAGGCTGATTTTATAC 52 TATGGTTAGCTGTGGCAGTGAGTGGTA 61 + ILLUMINA 0.795159865 210 FALSE ACP1 +snp_rs1049564 snp_rs1049564 snp_rs1049564 Homo sapiens hg19 chr14 20940526 20940576 + TTTCTCCCCCAGATACACCTATGAAGA 51 CTTTCCCCGAAGTACAGGTACTGGCAA 35 + ILLUMINA 0.881619662 192 FALSE ACP1 +snp_rs11094448 snp_rs11094448 snp_rs11094448 Homo sapiens hg19 chrX 147217312 147217367 + TGTGCCATGTCCTCTTAACATATAGCT 58 TCCAACCTTCTCTATGCAGTACATAGC 48 + ILLUMINA 0.854080172 197 FALSE ACP1 +snp_rs10852042 snp_rs10852042 snp_rs10852042 Homo sapiens hg19 chr15 96563051 96563103 + ACTCAACTACATAAACACCTTGTTCCC 42 CTACACCAAGTAAAATGGGTACATTTC 124 + ILLUMINA 0.457792624 194 FALSE ACP1 +snp_rs10492367 snp_rs10492367 snp_rs10492367 Homo sapiens hg19 chr12 28014882 28014943 + TCATCTTTTCGGCTCTTCTTGTCTCTG 38 GAACATGGTTTCATCAGTTTGAGCTAC 80 + ILLUMINA 0.738003928 203 FALSE ACP1 +snp_rs10519420 snp_rs10519420 snp_rs10519420 Homo sapiens hg19 chr4 138313081 138313150 + CATCATGTGAACCACTGCCTGTCGTTT 51 AGGAAAGAGTTAGACAAGGTGAATGCA 69 + ILLUMINA 0.73924162 211 FALSE ACP1 +snp_rs10278557 snp_rs10278557 snp_rs10278557 Homo sapiens hg19 chr7 15698951 15699007 + TTATTTTAAAATATGAAAGGTGTGGAAACC 819 TCAAAGTATCTGTAATGTCTAAACCCAG 94 + ILLUMINA 6.32E-27 198 FALSE ACP1 +snp_rs11017144 snp_rs11017144 snp_rs11017144 Homo sapiens hg19 chr10 132012880 132012933 + AAGGTCTGGGCATGGGAGGGCCCATTTT 73 ACTAGGATGTATTTCAGCATGTCTCGC 66 + ILLUMINA 0.664913089 195 FALSE ACP1 +snp_rs12651141 snp_rs12651141 snp_rs12651141 Homo sapiens hg19 chr4 89287627 89287677 + AACTAAGCATATTAGGGAGTGTGTTCT 39 TGTTCTTCTACTTGCCTCTGGAGGAT 67 + ILLUMINA 0.761725294 192 FALSE ACP1 +snp_rs1040247 snp_rs1040247 snp_rs1040247 Homo sapiens hg19 chr8 139533282 139533337 + GGCGGGGATTTGGGTCATTTATTGTT 48 CCTTAGCATGACAACCAAAGCAGCTA 59 + ILLUMINA 0.831417646 197 FALSE ACP1 +snp_rs10103493 snp_rs10103493 snp_rs10103493 Homo sapiens hg19 chr8 97352457 97352513 + CCACGCCTGCCGGAGCATCTATGACAA 14 TCACCCTTTGTGTCTTCCTGCCGCTTT 59 + ILLUMINA 0.578108916 198 FALSE ACP1 +snp_rs10180924 snp_rs10180924 snp_rs10180924 Homo sapiens hg19 chr2 86021832 86021893 + CAGCTCAGTGTTGGTGCCATCTGTCA 56 TTCCCTGTCAGCACCTCCCACGGAGA 53 + ILLUMINA 0.552464345 203 FALSE ACP1 +snp_rs10061008 snp_rs10061008 snp_rs10061008 Homo sapiens hg19 chr5 141744430 141744481 + TGCACGTTTCACAGTGAATGAAGGAAC 59 TCCTCAGCCTTCCTTCCTCGATGCTT 73 + ILLUMINA 0.79197988 193 FALSE ACP1 +snp_rs12570664 snp_rs12570664 snp_rs12570664 Homo sapiens hg19 chr10 1816215 1816270 + GCAAGAATTGAGTTGCTGCAGACTCA 108 ACTACTCCTGGCACTTAAATCTCAGAC 68 + ILLUMINA 0.617083905 197 FALSE ACP1 +snp_rs11017185 snp_rs11017185 snp_rs11017185 Homo sapiens hg19 chr10 132096075 132096165 + TCCTCTAATGCCGCTGGGTTAGG 184 AAAACCACAAACAGGAATCTCCTTGGG 63 + ILLUMINA 0.041126589 232 FALSE ACP1 +snp_rs10252308 snp_rs10252308 snp_rs10252308 Homo sapiens hg19 chr7 148501622 148501670 + GAGGTTGGAAACAGTATCACAGCAAC 57 TGCTGTGACCTAAGGGAACAAGGGAA 83 + ILLUMINA 0.806848985 190 FALSE ACP1 +snp_rs10490542 snp_rs10490542 snp_rs10490542 Homo sapiens hg19 chr2 207587227 207587313 + AGTCTGGGGTATGAGAACGAACTAA 34 CAGCTTTGAAAAGTTAGTATGACATCC 93 + ILLUMINA 0.331894043 228 FALSE ACP1 +snp_rs10776798 snp_rs10776798 snp_rs10776798 Homo sapiens hg19 chr1 115862165 115862222 + TACTGCAAAACCCTCGCCTCTGGGAT 25 AGTATGAACTCTGACCCCTACTCACCT 53 + ILLUMINA 0.719405389 199 FALSE ACP1 +snp_rs10894631 snp_rs10894631 snp_rs10894631 Homo sapiens hg19 chr11 132829598 132829646 + CATCCTAGTGGTTCACAGCGTTTCCAT 25 CCTGCTAACATAGCAGCCTGAGGA 55 + ILLUMINA 0.644587764 190 FALSE ACP1 +snp_rs10505173 snp_rs10505173 snp_rs10505173 Homo sapiens hg19 chr8 113486133 113486202 + TTCAGATTAGGAGCCATCCTTCTTGC 82 TTTTGCAGGAAGGACAGAGTACAATTT 101 + ILLUMINA 0.449201677 211 FALSE ACP1 +snp_rs10016530 snp_rs10016530 snp_rs10016530 Homo sapiens hg19 chr4 183824878 183824969 + TCTGAGGGAAGCCTCCACACCCA 54 CCTCAGCCTCCGGACCTAAGAAATAGA 103 + ILLUMINA 0.166741199 233 FALSE ACP1 +snp_rs11125183 snp_rs11125183 snp_rs11125183 Homo sapiens hg19 chr2 49013567 49013628 + CTCCTTTGAAGTAGCTTATCATGAGTC 47 ATCAAACCTCTTAGTGATGGCATACCC 37 + ILLUMINA 0.799737951 203 FALSE ACP1 +snp_rs10113311 snp_rs10113311 snp_rs10113311 Homo sapiens hg19 chr8 61888372 61888437 + CCCCTCTTCCTGCATTGTCTTCTT 135 CAGGAGCCAAGAGCTAAGTGAAGAGTA 80 + ILLUMINA 0.238729124 207 FALSE ACP1 +snp_rs10516939 snp_rs10516939 snp_rs10516939 Homo sapiens hg19 chr4 94574620 94574670 + CTCTTGAACTCTGAAACCCGAGAATGC 46 TCTCCAGCCTTGACGTCCCTGAAGAA 98 + ILLUMINA 0.674947194 192 FALSE ACP1 +snp_rs10790866 snp_rs10790866 snp_rs10790866 Homo sapiens hg19 chr11 127063152 127063229 + GAAGCTGCTTCCCAGAGTAAAAATGTG 68 AAGGGGGAGAGGCGTGTCACCTCCTTAT 44 + ILLUMINA 0.549780598 219 FALSE ACP1 +snp_rs1029864 snp_rs1029864 snp_rs1029864 Homo sapiens hg19 chr2 107784306 107784374 + TGTTATTGTATGGATCTGTTTCTTTTACC 141 TTATCTCAATCTAAACTGAGCAGACGG 36 + ILLUMINA 0.221138512 210 FALSE ACP1 +snp_rs10869715 snp_rs10869715 snp_rs10869715 Homo sapiens hg19 chr9 78780394 78780456 + AGAATGCTGTGGCCTTGATACATTCAC 45 ATAGGGCTGTGGGGCACCATTTCAATA 50 + ILLUMINA 0.854109314 204 FALSE ACP1 +snp_rs10248924 snp_rs10248924 snp_rs10248924 Homo sapiens hg19 chr7 138831626 138831699 + ATGTTACCAGGTAATAGTAAAGAGAGTAG 51 GAAGACAAAGAACCTAAGGGAAATAGG 105 + ILLUMINA 0.334366493 215 FALSE ACP1 +snp_rs10836419 snp_rs10836419 snp_rs10836419 Homo sapiens hg19 chr11 35580595 35580696 + AGCTAGCCTCCTTAAGAAGAGTAAAAG 50 AATGAATTGGCAATCAGAATCAACACC 75 + ILLUMINA 0.295688457 243 FALSE ACP1 +snp_rs10484150 snp_rs10484150 snp_rs10484150 Homo sapiens hg19 chr14 83637845 83637921 + GTGTAGGGCATGTTGAGAAGAAAACAC 67 AAAGATGTAGGATATACTGGATCCCGG 31 + ILLUMINA 0.6384027 218 FALSE ACP1 +snp_rs12719046 snp_rs12719046 snp_rs12719046 Homo sapiens hg19 chr7 51334392 51334472 + AAAGTGAGAAACGGCTTTTCTGGCTG 52 ATTGAGATAACCCAATTCAGGGTTGGG 55 + ILLUMINA 0.579925547 222 FALSE ACP1 +snp_rs1152562 snp_rs1152562 snp_rs1152562 Homo sapiens hg19 chr14 56879046 56879117 + CACTCTGCCATTAGAGAGAAGCAACT 70 ACAAGAAGACGGGTGGGTACTGCTCA 27 + ILLUMINA 0.499059095 213 FALSE ACP1 +snp_rs12679346 snp_rs12679346 snp_rs12679346 Homo sapiens hg19 chr8 34068371 34068443 + AATCAGGTACAGAGAGTATTGCAGAGT 49 ATGGCAACTGTAAGATTGATATGTGCG 34 + ILLUMINA 0.66746334 214 FALSE ACP1 +snp_rs11095604 snp_rs11095604 snp_rs11095604 Homo sapiens hg19 chrX 13143811 13143869 + CCACTGGCACATCTTCCTTGTTTTCA 65 GTCAAGAAGGAACACCCCATTATTCTC 53 + ILLUMINA 0.813724664 200 FALSE ACP1 +snp_rs10059981 snp_rs10059981 snp_rs10059981 Homo sapiens hg19 chr5 3619439 3619487 + CCATCACTGCACATGACAGGTGCTCA 70 TGTTGTCTCTCTAGCTTGGAGGACCAA 62 + ILLUMINA 0.782154177 190 FALSE ACP1 +snp_rs11070073 snp_rs11070073 snp_rs11070073 Homo sapiens hg19 chr13 94692842 94692897 + AATGCCTTCTGCTTAGCCCATTAAAGG 42 TGAAAGGCTGAGCCTATAGGCTGCATT 31 + ILLUMINA 0.843852663 197 FALSE ACP1 +snp_rs1144171 snp_rs1144171 snp_rs1144171 Homo sapiens hg19 chr6 91698172 91698250 + CAGGCCATATGCTGCCAAAGGAAACAA 51 TCTTTTCAGGCTATCCCATTTTCTGGC 82 + ILLUMINA 0.616778652 220 FALSE ACP1 +snp_rs1049269 snp_rs1049269 snp_rs1049269 Homo sapiens hg19 chr10 73819921 73819985 + GTCACAAATCAAGGAGCTGAGGAAGGA 68 AAACAGGCAAGGCTGGACCCCTGCAAT 60 + ILLUMINA 0.63914031 206 FALSE ACP1 +snp_rs10263803 snp_rs10263803 snp_rs10263803 Homo sapiens hg19 chr7 20437741 20437792 + ACATTAAAGGTAGCTGGATCCTTTGGA 54 TTAAGGATTGCAGCAAGCTTGACTGAC 43 + ILLUMINA 0.862933678 193 FALSE ACP1 +snp_rs11121704 snp_rs11121704 snp_rs11121704 Homo sapiens hg19 chr1 11293865 11293936 + TCTCAGTGATTGTTCATCCAGATTAAC 48 AACTCTTACCTCTTGTAAGGACAGCAC 76 + ILLUMINA 0.627370892 213 FALSE ACP1 +snp_rs10471977 snp_rs10471977 snp_rs10471977 Homo sapiens hg19 chr5 55750304 55750352 + CAGCGTTCAGTTCTCCTTAATTACAGG 50 AAGTCTTGACACCGCTCGGCAAGATCT 12 + ILLUMINA 0.767369442 190 FALSE ACP1 +snp_rs1005790 snp_rs1005790 snp_rs1005790 Homo sapiens hg19 chr5 160174868 160174920 + CACAGCGCTGTCATAGCTGTCTTTCAT 33 ATGAAGAGGTATCTGGGTCCAGCTGA 52 + ILLUMINA 0.829704017 194 FALSE ACP1 +snp_rs10863725 snp_rs10863725 snp_rs10863725 Homo sapiens hg19 chr1 208950718 208950838 + TCAGACTTCTTGCCACCAGAACTGT 162 GGAAGAGAAAGAGTCCATATAACATTGG 93 + ILLUMINA 0.033824951 262 FALSE ACP1 +snp_rs10930259 snp_rs10930259 snp_rs10930259 Homo sapiens hg19 chr2 167842556 167842611 + ACTGATGGAACTAGGAAGCTATAACCC 34 AAACTGATGAGGTTCTTTTGTGGCAC 76 + ILLUMINA 0.789566247 197 FALSE ACP1 +snp_rs10813743 snp_rs10813743 snp_rs10813743 Homo sapiens hg19 chr9 32109969 32110042 + TTTGCTCTGTCCAAGGGCCACAGCATTTT 72 AGAGATGAGCATGACTTGTGAGGTTAG 44 + ILLUMINA 0.54080386 215 FALSE ACP1 +snp_rs10906498 snp_rs10906498 snp_rs10906498 Homo sapiens hg19 chr10 13859315 13859378 + AGGAGAGGAGCTCTCAGTCAGTGCTTT 68 TCAAAACAGCACTTAACGTGTTGCAGG 33 + ILLUMINA 0.716514314 205 FALSE ACP1 +snp_rs10195834 snp_rs10195834 snp_rs10195834 Homo sapiens hg19 chr2 66826978 66827029 + ACCCTCTCCTTGCTCTTTTCCT 148 GGGAAAGCCTGTAAAGCTCTGAGGTTA 65 + ILLUMINA 0.159820735 193 FALSE ACP1 +snp_rs10248887 snp_rs10248887 snp_rs10248887 Homo sapiens hg19 chr7 23711688 23711734 + GAAGGTAAGTTTATAGGCACACTGGAG 32 TTCTCATGAAGAACTGCTGGGGCTAT 52 + ILLUMINA 0.859839636 188 FALSE ACP1 +snp_rs10135821 snp_rs10135821 snp_rs10135821 Homo sapiens hg19 chr14 97199808 97199866 + GTTTCTAGACTTGCCTCTTCATCCAGC 63 TTTGCTCACATTTCAGAGCTTCCGTTC 60 + ILLUMINA 0.839261548 200 FALSE ACP1 +snp_rs10999042 snp_rs10999042 snp_rs10999042 Homo sapiens hg19 chr10 71707334 71707381 + AGCCTGGGGCCTGATCCTCACATGGAA 63 AGATCCATTGCTACCTTGTCCTTGC 38 + ILLUMINA 0.642754309 189 FALSE ACP1 +snp_rs10036347 snp_rs10036347 snp_rs10036347 Homo sapiens hg19 chr5 56694562 56694640 + TAACGTGGCATTGTCATTCAACTTATT 40 ATTAAAAAGCAGTTGGTGATGTGAGAC 84 + ILLUMINA 0.4353583 220 FALSE ACP1 +snp_rs10189159 snp_rs10189159 snp_rs10189159 Homo sapiens hg19 chr2 50714476 50714545 + CAGGTCTTTCTGACGTCAAAGACTGT 88 TAAGGAGCACTGGAAGTACCCTCTAGT 31 + ILLUMINA 0.608621013 211 FALSE ACP1 +snp_rs10491907 snp_rs10491907 snp_rs10491907 Homo sapiens hg19 chr9 9963859 9963931 + TGAAGGGTACCATGCACTAACTCAATG 23 GCATTAATATATATGAATGGCACATCAGAG 198 + ILLUMINA 0.049106968 214 FALSE ACP1 +snp_rs10737814 snp_rs10737814 snp_rs10737814 Homo sapiens hg19 chr1 237469221 237469276 + TTCTTCAACCTGGTTGATGGACTCATG 49 AATGTTGGCAATACATGAAAAATTATGTC 285 + ILLUMINA 0.002100647 197 FALSE ACP1 +snp_rs10503087 snp_rs10503087 snp_rs10503087 Homo sapiens hg19 chr18 61476361 61476445 + AGTGATCCGAATGGAAAGGGAAGTGT 21 TGTGATGAGTGAGGGCAGATGAGCTAT 72 + ILLUMINA 0.484485528 226 FALSE ACP1 +snp_rs10094564 snp_rs10094564 snp_rs10094564 Homo sapiens hg19 chr8 673456 673552 + TCCACTTAATAGACTTACAAACAGAAAAG 120 TGCTCTCTCAGTGAACAGCAGCTCTA 84 + ILLUMINA 0.160482166 238 FALSE ACP1 +snp_rs11662907 snp_rs11662907 snp_rs11662907 Homo sapiens hg19 chr18 21455480 21455528 + AGGAAACAAGACCAACCCAAGGAGA 68 CTGATTGTGGCATGATTGTCTAAATCTC 69 + ILLUMINA 0.697121256 190 FALSE ACP1 +snp_rs10093381 snp_rs10093381 snp_rs10093381 Homo sapiens hg19 chr8 87628292 87628377 + CAGGGACAGATAGCAGCAGTGAAGGAA 60 CTTTTTATTAACATACTTGGATAGCACATG 95 + ILLUMINA 0.190601841 227 FALSE ACP1 +snp_rs10741808 snp_rs10741808 snp_rs10741808 Homo sapiens hg19 chr11 20020803 20020858 + TGCCTGGCATAAATCAACCCTGCTGTT 41 TGCTTTGGGAAAATGTGGGGTTT 113 + ILLUMINA 0.354015863 197 FALSE ACP1 +snp_rs11563212 snp_rs11563212 snp_rs11563212 Homo sapiens hg19 chr2 234869276 234869363 + CCATTCTCCTGTTTAGAGGTTTGAACTG 59 CTTTCTCCTTAGTCTGCTGACCTTCA 41 + ILLUMINA 0.34051809 229 FALSE ACP1 +snp_rs10514496 snp_rs10514496 snp_rs10514496 Homo sapiens hg19 chr16 80456324 80456376 + GTTTGAGAAATGCGATTTTCTGAGTCC 43 TCATGTTTCTGGTGGCATGCTCGGTT 25 + ILLUMINA 0.816692977 194 FALSE ACP1 +snp_rs11633318 snp_rs11633318 snp_rs11633318 Homo sapiens hg19 chr15 77602616 77602693 + GTTTAAACTTATGGCCAAATCTGGATG 40 TTCTCTGCAGGTTTCATATCAAAGCAC 82 + ILLUMINA 0.441984635 219 FALSE ACP1 +snp_rs10509550 snp_rs10509550 snp_rs10509550 Homo sapiens hg19 chr10 90219207 90219273 + CAAGACCAAATCCACTACTTTTATTGG 54 ATTTTAGAGTCAACAGAGCCCCAGGA 89 + ILLUMINA 0.596984845 208 FALSE ACP1 +snp_rs10758 snp_rs10758 snp_rs10758 Homo sapiens hg19 chr2 113409907 113409988 + GGCGTACGCATAGTCTGCATGTTGTAT 9 TATCAGTCACTGGTACAGTTAGTCTTG 50 + ILLUMINA 0.43987156 223 FALSE ACP1 +snp_rs10281519 snp_rs10281519 snp_rs10281519 Homo sapiens hg19 chr7 90909948 90909993 + CCTTCCCAGGGAATTCACTAATCA 53 CTGGGAAATGTGAGTAAGACAGGACT 81 + ILLUMINA 0.642655414 187 FALSE ACP1 +snp_rs10860784 snp_rs10860784 snp_rs10860784 Homo sapiens hg19 chr12 102172954 102173002 + AACTGCTCTCTAGTCACCTCTAATCAC 39 AACTAGAGCCTCACAAATTCTGAGACA 76 + ILLUMINA 0.833925354 190 FALSE ACP1 +snp_rs11077405 snp_rs11077405 snp_rs11077405 Homo sapiens hg19 chr17 76969792 76969858 + ATTTTAGAACTCCGGGGGTCCTCGA 22 TGAAGTAACTGTGACCTTTCAACCAGG 55 + ILLUMINA 0.631855495 208 FALSE ACP1 +snp_rs10449246 snp_rs10449246 snp_rs10449246 Homo sapiens hg19 chr1 224936216 224936267 + GGAGCGCTAATGCATAATTTTGTGAGG 32 ATGGCTGTATCTGAGAATATTGGATGA 87 + ILLUMINA 0.708845715 193 FALSE ACP1 +snp_rs10185855 snp_rs10185855 snp_rs10185855 Homo sapiens hg19 chr2 101642181 101642232 + AAGTCTTACGCAGAACATGAAAGGAAG 40 GCTTACGCACCAAGTCTGTATTTATAC 84 + ILLUMINA 0.736144802 193 FALSE ACP1 +snp_rs10184153 snp_rs10184153 snp_rs10184153 Homo sapiens hg19 chr2 182220086 182220159 + GTTTTCTGAGACCAGATTATTTTCCTGG 108 GTCAAAAACTAATCGTGTATATGTCTGC 35 + ILLUMINA 0.402172069 215 FALSE ACP1 +snp_rs10771328 snp_rs10771328 snp_rs10771328 Homo sapiens hg19 chr12 27425285 27425341 + AGAATTAGCACAGCGTTGGAATGACC 28 AGGAAGGACTGGGAAAGTAGCTCTTT 80 + ILLUMINA 0.724169864 198 FALSE ACP1 +snp_rs11563675 snp_rs11563675 snp_rs11563675 Homo sapiens hg19 chr7 126873844 126873897 + CCAGAGGGAGCCTTGAAGCGTCTTAGA 43 CAGCCTGGTGTTCCTTATGTATTCAAG 96 + ILLUMINA 0.670020123 195 FALSE ACP1 +snp_rs10148795 snp_rs10148795 snp_rs10148795 Homo sapiens hg19 chr14 33845222 33845303 + GCATCACTCTGACCCTGGCATTTATT 59 ACCGTTATTTCCCTATATTGTACTGCC 54 + ILLUMINA 0.564029693 223 FALSE ACP1 +snp_rs10516506 snp_rs10516506 snp_rs10516506 Homo sapiens hg19 chr4 104595153 104595243 + CCAAATGTGTACAACTCCATTCAATTTC 121 GAGGCAGAACACTTGGAAGCTTTAGT 61 + ILLUMINA 0.251340571 232 FALSE ACP1 +snp_rs10178199 snp_rs10178199 snp_rs10178199 Homo sapiens hg19 chr2 127756865 127756948 + GGGAGCCCCTCCTGGAAAATATGAAA 52 GTTGGCAGGCAACCTGGGATCCAGGTA 52 + ILLUMINA 0.440003964 225 FALSE ACP1 +snp_rs10516603 snp_rs10516603 snp_rs10516603 Homo sapiens hg19 chr4 115467380 115467430 + TTTTGTCACTAGTCTTCTTCGGATAAG 51 ATACTTTGACACCGCCCTTTCATTTTT 69 + ILLUMINA 0.702227708 192 FALSE ACP1 +snp_rs10088698 snp_rs10088698 snp_rs10088698 Homo sapiens hg19 chr8 48654691 48654751 + ACGCACCCCTCATGCTGTTAAAGCTT 52 TACCTGCTCACATTCTCCTCAACAGA 97 + ILLUMINA 0.589067948 202 FALSE ACP1 +snp_rs10103826 snp_rs10103826 snp_rs10103826 Homo sapiens hg19 chr8 135495979 135496032 + AGCAGCATAGATAGCTCGATAGAAACC 40 TCCCCTTGAGACCCCATGTCTTCCTT 64 + ILLUMINA 0.817672011 195 FALSE ACP1 +snp_rs1042606 snp_rs1042606 snp_rs1042606 Homo sapiens hg19 chr10 112270593 112270642 + AAAGAAGTTGCTGGACCAGGAGAAAAG 62 TTTGTAGGGACATGATCAGCATCCTG 46 + ILLUMINA 0.870011729 191 FALSE ACP1 +snp_rs10497276 snp_rs10497276 snp_rs10497276 Homo sapiens hg19 chr2 166856914 166856971 + TCAAAACATTTAGAAATAACCCCCTATTC 278 GAATTTTGAGTCCTGTGGGCCTAAAAG 47 + ILLUMINA 0.003394502 199 FALSE ACP1 +snp_rs10753764 snp_rs10753764 snp_rs10753764 Homo sapiens hg19 chr1 167760634 167760737 + CCTACACTGAGAACAATCCTGTGCCAA 45 TGTTTGAAAGATTATATGGCTTACCCA 98 + ILLUMINA 0.204817817 245 FALSE ACP1 +snp_rs1002745 snp_rs1002745 snp_rs1002745 Homo sapiens hg19 chr10 82656204 82656270 + TCCAGCAAAGCCCCACGGCATTATAAA 32 CAGGGAAATTGGAGCAGAAGCTTGGT 79 + ILLUMINA 0.613980515 208 FALSE ACP1 +snp_rs10073948 snp_rs10073948 snp_rs10073948 Homo sapiens hg19 chr5 82134537 82134591 + CTGCAATACCTCAACTGAGAAGGGCTTA 39 TGACAACAAAGGACAGGGGGTGTTGAA 53 + ILLUMINA 0.854008791 196 FALSE ACP1 +snp_rs10830004 snp_rs10830004 snp_rs10830004 Homo sapiens hg19 chr10 133212128 133212221 + GACCTTGTGCTGTGCATGTTTTCCTT 66 CTAAATACACTTCAGAAGAGATGGGCA 109 + ILLUMINA 0.296586818 235 FALSE ACP1 +snp_rs10128762 snp_rs10128762 snp_rs10128762 Homo sapiens hg19 chr12 74681809 74681869 + TCCACAGGAGGTATTGAAGCTCGTTA 37 AAATCAAGGCACATCTCTAGTTATTTTC 125 + ILLUMINA 0.347800351 202 FALSE ACP1 +snp_rs10109209 snp_rs10109209 snp_rs10109209 Homo sapiens hg19 chr8 5528860 5528911 + AGCGTGGTAATGTGTGGCACAGGTGAT 25 TGTCCTAGAGCAATGAAAGACGCTGT 32 + ILLUMINA 0.771242335 193 FALSE ACP1 +snp_rs1026580 snp_rs1026580 snp_rs1026580 Homo sapiens hg19 chr10 13981069 13981144 + TAGAATTCCCAGAATAGCACCATCCTC 51 AATTGCCTGGGATTAATCAATGTAGGG 41 + ILLUMINA 0.722675516 217 FALSE ACP1 +snp_rs10505299 snp_rs10505299 snp_rs10505299 Homo sapiens hg19 chr8 118426643 118426707 + CCACTTTCATATTAACCCCCACAAAAT 42 CAAGCAATGTATTGCTCCCTCTGTTG 54 + ILLUMINA 0.647721082 206 FALSE ACP1 +snp_rs10919336 snp_rs10919336 snp_rs10919336 Homo sapiens hg19 chr1 170216721 170216792 + CTCCCCCTGAAGCAAATCCTAAACCAA 68 AAGTTAGAAGCATTTAATGAAATAAAGCAG 610 + ILLUMINA 8.64E-15 213 FALSE ACP1 +snp_rs10505532 snp_rs10505532 snp_rs10505532 Homo sapiens hg19 chr8 130021864 130021933 + GACTCCTGATACACAGAAATTTGAGTT 79 GTTCTAACAACACCTAATCTGTTTCTC 91 + ILLUMINA 0.46771952 211 FALSE ACP1 +snp_rs10518287 snp_rs10518287 snp_rs10518287 Homo sapiens hg19 chr19 35399305 35399389 + GATGTGCTCCACCATGTAACGACATA 42 AAAAGTCCCTGTATTCCTGTCTCCCA 91 + ILLUMINA 0.44819409 226 FALSE ACP1 +snp_rs10955157 snp_rs10955157 snp_rs10955157 Homo sapiens hg19 chr8 99227053 99227147 + TCTAATATGGAAGATGAACTCATCCCT 80 GTTAACAGAAATATCCCTCTGGGCCCA 69 + ILLUMINA 0.358330774 236 FALSE ACP1 +snp_rs10487324 snp_rs10487324 snp_rs10487324 Homo sapiens hg19 chr7 110036520 110036568 + GATTAGGGGCCATGTTTCCTGGAATAG 41 ACTGTTCTGGGTCATTTAGGTCAGAC 54 + ILLUMINA 0.910875574 190 FALSE ACP1 +snp_rs10519096 snp_rs10519096 snp_rs10519096 Homo sapiens hg19 chr15 61289830 61289923 + GCTGCTTCTCAAATAGTGTGTTTTAAA 100 TTTTCTCCCATCTGGACCTTGAAGT 61 + ILLUMINA 0.211654611 235 FALSE ACP1 +snp_rs10968281 snp_rs10968281 snp_rs10968281 Homo sapiens hg19 chr9 28013206 28013269 + CACTGGGTCTCTAGTAACAATCAGGAT 54 GAAGGGTCTTATGATCCAGACGATTGT 23 + ILLUMINA 0.755247179 205 FALSE ACP1 +snp_rs11060670 snp_rs11060670 snp_rs11060670 Homo sapiens hg19 chr12 130515637 130515690 + TCTCCCATCTTGTGCCCCTCCTCAGAT 77 CATCACCGGGAGTCCTGAGAGCTCAT 37 + ILLUMINA 0.645938591 195 FALSE ACP1 +snp_rs10859402 snp_rs10859402 snp_rs10859402 Homo sapiens hg19 chr12 93409765 93409825 + TGAGGTTGTTCATGCAAAGGGATCCA 45 TGCAGGGAGGGAATTTTCATGCAATC 68 + ILLUMINA 0.749309572 202 FALSE ACP1 +snp_rs1108958 snp_rs1108958 snp_rs1108958 Homo sapiens hg19 chr13 51822103 51822156 + ATGTTCAACCAAACCGAAAGAAGCCAG 35 TGATCTGAAAGTAACTGGCCCATCCT 38 + ILLUMINA 0.827366875 195 FALSE ACP1 +snp_rs10869756 snp_rs10869756 snp_rs10869756 Homo sapiens hg19 chr9 78959243 78959314 + GTAAACCAATCCAGGCAGAGCTGCTCA 82 AAGAATTAGCCTTCCAAACAAACTGCA 101 + ILLUMINA 0.430023894 213 FALSE ACP1 +snp_rs10502370 snp_rs10502370 snp_rs10502370 Homo sapiens hg19 chr18 8454421 8454471 + GATCACATCTCTCTGGACATACCCTCA 47 ACTCTGTGATTGACAAATCTTTCACCT 71 + ILLUMINA 0.784698937 192 FALSE ACP1 +snp_rs10000030 snp_rs10000030 snp_rs10000030 Homo sapiens hg19 chr4 103374075 103374128 + TGATGTCTTCCTTCTTTTTAGGCAAAA 218 ACCAATATCTATGAATCTGTATAGCTTGG 112 + ILLUMINA 0.022909171 195 FALSE ACP1 +snp_rs10746432 snp_rs10746432 snp_rs10746432 Homo sapiens hg19 chr1 210837610 210837664 + GCCTCATAGGCTTATTAAGATTAAAACTC 69 CTGAACATGGTTAAACTAAGTGCTGTC 50 + ILLUMINA 0.622318136 196 FALSE ACP1 +snp_rs10438441 snp_rs10438441 snp_rs10438441 Homo sapiens hg19 chr15 92862529 92862587 + AGCCTCTCAACTTCCCACCGAGCATGT 43 AGCTCTCCTCCCAGTATCCCCCATATA 63 + ILLUMINA 0.721013335 200 FALSE ACP1 +snp_rs1110240 snp_rs1110240 snp_rs1110240 Homo sapiens hg19 chr1 21324849 21324927 + AATACAAGGCATGTCAAGGCAAACAGC 46 TTCCTCAGCTAAATCATAGAGTACTTG 58 + ILLUMINA 0.513382127 220 FALSE ACP1 +snp_rs10110604 snp_rs10110604 snp_rs10110604 Homo sapiens hg19 chr8 16502996 16503053 + GCTGCACAGTTGTCTTAGTTTTCTCC 51 TTGGCAAGGGTCAATACACATTGGTTC 43 + ILLUMINA 0.843584667 199 FALSE ACP1 +snp_rs10502432 snp_rs10502432 snp_rs10502432 Homo sapiens hg19 chr18 19827394 19827445 + GTGCTCAGGGTTCTGGAGTTTTGACAA 48 TTTCTGTCAAGCTGGACATGATTCTGC 56 + ILLUMINA 0.917357342 193 FALSE ACP1 +snp_rs10874743 snp_rs10874743 snp_rs10874743 Homo sapiens hg19 chr1 91952023 91952090 + GAAACTGTGACAGGCAAACTTGTTAGC 74 CTTCAACCTGTGAAGTGTTCCTCTAGC 48 + ILLUMINA 0.701461162 209 FALSE ACP1 +snp_rs10090419 snp_rs10090419 snp_rs10090419 Homo sapiens hg19 chr8 124028550 124028599 + GCTAAGAGAACTTAAACCCAAGCCTAC 59 TCCGCTTAAACCCTTCTTGGCAGCAA 57 + ILLUMINA 0.876469624 191 FALSE ACP1 +snp_rs10496687 snp_rs10496687 snp_rs10496687 Homo sapiens hg19 chr2 133269176 133269237 + GTGTGAGTAGGGTTCACAAATCAAAAA 30 ACACTGACTTAATATGTACTACGTGCC 50 + ILLUMINA 0.710425199 203 FALSE ACP1 +snp_rs10790037 snp_rs10790037 snp_rs10790037 Homo sapiens hg19 chr11 114665080 114665137 + TCTCATTCTAGATGAAGCACCCTTCCC 54 TGTGAATGTGTACCTACCACACCAG 50 + ILLUMINA 0.760277944 199 FALSE ACP1 +snp_rs10895457 snp_rs10895457 snp_rs10895457 Homo sapiens hg19 chr11 103416570 103416625 + GAGGTCAATGCAATACAGAAGTGTAGC 70 GCTGGTTGTCATGACATTAATGCTACC 40 + ILLUMINA 0.838645904 197 FALSE ACP1 +snp_rs12604608 snp_rs12604608 snp_rs12604608 Homo sapiens hg19 chr18 42405998 42406053 + AAAGAGTGACTAGTACCTTGATGTTTC 39 GAGTTCAAAGGAAAGTTCTAGTGTAATG 98 + ILLUMINA 0.521149416 197 FALSE ACP1 +snp_rs11171681 snp_rs11171681 snp_rs11171681 Homo sapiens hg19 chr12 56193146 56193212 + TGTTCAAAGTTTAGGACTCAACGGCTC 35 CAAGAGAGAACAGAGTGCTACTTCAGA 72 + ILLUMINA 0.753497256 208 FALSE ACP1 +snp_rs10961505 snp_rs10961505 snp_rs10961505 Homo sapiens hg19 chr9 14410504 14410576 + AGGGCAGAGTAAACTACTATGCATAAGG 49 AACAAAGAGGTTGAAGGTTATGAGCAG 113 + ILLUMINA 0.472851967 214 FALSE ACP1 +snp_rs10497933 snp_rs10497933 snp_rs10497933 Homo sapiens hg19 chr2 212141596 212141648 + GCCTGCCTTCAAGTGTTTGAAAGCTT 72 CTTGAAGAGAAGACCATTGATCTGACA 44 + ILLUMINA 0.815850902 194 FALSE ACP1 +snp_rs12587583 snp_rs12587583 snp_rs12587583 Homo sapiens hg19 chr14 69510363 69510412 + GAAGAAAGTGACTTGGCCCATGCCT 51 AGAGCATGAGGGGAAGAGGTTTCTT 81 + ILLUMINA 0.655533052 191 FALSE ACP1 +snp_rs10966009 snp_rs10966009 snp_rs10966009 Homo sapiens hg19 chr9 23651348 23651413 + TGATGCACAGTCCTGAGTCCTACGAAT 37 GGGATGCAGTGGTGGCAAGAAGTAA 95 + ILLUMINA 0.531626857 207 FALSE ACP1 +snp_rs1160246 snp_rs1160246 snp_rs1160246 Homo sapiens hg19 chr9 119993006 119993061 + AGCAACCCATAGTAAGTGAACCAAAGAG 42 AGAGAAGGCTGTGGACTGAAAACAA 116 + ILLUMINA 0.496012169 197 FALSE ACP1 +snp_rs11096672 snp_rs11096672 snp_rs11096672 Homo sapiens hg19 chr2 20743635 20743702 + AGGGGATTGCTCCAAACTTTGCTAAC 37 CAGCGTTCCCTCTCACAGGAGCTATTA 55 + ILLUMINA 0.707692541 209 FALSE ACP1 +snp_rs10926264 snp_rs10926264 snp_rs10926264 Homo sapiens hg19 chr1 235779057 235779105 + ATGAACATCACATAGACATAGCCATTA 61 AAGGTCGTGGTGGGCTCACTCTCTGT 35 + ILLUMINA 0.585085977 190 FALSE ACP1 +snp_rs10050018 snp_rs10050018 snp_rs10050018 Homo sapiens hg19 chr4 183349539 183349586 + GTCAACAATTGTTCACTCAAGGAAGTG 39 AGGATCTGATCAATTTGATGAGTCTTT 81 + ILLUMINA 0.654680237 189 FALSE ACP1 +snp_rs10243669 snp_rs10243669 snp_rs10243669 Homo sapiens hg19 chr7 45915829 45915895 + CATCAGGGTGAGGCCATGTTGAATCT 49 CAGAAAAATCTGATGTGGCAGGTGCT 72 + ILLUMINA 0.639578438 208 FALSE ACP1 +snp_rs10767843 snp_rs10767843 snp_rs10767843 Homo sapiens hg19 chr11 30436295 30436376 + CCTCAATTCAGTTACTTTCGCTATTTT 66 TGTCCTCTCCAGCGACAGGCAAAAAT 76 + ILLUMINA 0.397654228 223 FALSE ACP1 +snp_rs1040173 snp_rs1040173 snp_rs1040173 Homo sapiens hg19 chr2 146120432 146120479 + GGACAAAGGGAGTATGGAACATTTGAG 38 AGGGGAATACAACATGATTTGGATGC 76 + ILLUMINA 0.799758636 189 FALSE ACP1 +snp_rs10490012 snp_rs10490012 snp_rs10490012 Homo sapiens hg19 chr2 234843415 234843500 + CAGCACTTCAAGAAGATCACTATCAGC 48 GTAAATGAAAATGTGACCTCCTGCCA 116 + ILLUMINA 0.217168479 227 FALSE ACP1 +snp_rs10500844 snp_rs10500844 snp_rs10500844 Homo sapiens hg19 chr11 19250076 19250155 + TCATGGAATAAATTCACTTAACCCCAC 84 AAAATAGCTTGTATTAAGAGCAGGGGC 75 + ILLUMINA 0.449062088 221 FALSE ACP1 +snp_rs10143478 snp_rs10143478 snp_rs10143478 Homo sapiens hg19 chr14 33442533 33442626 + GTGGGGTAGTATGGGGTTTTTGTCTCT 46 CAGAATTTTGTTAGTAAGTTTGGAATTGC 114 + ILLUMINA 0.185383354 235 FALSE ACP1 +snp_rs10493230 snp_rs10493230 snp_rs10493230 Homo sapiens hg19 chr1 58050024 58050109 + GTGAATCTGTTGTGATTCTGCAGGCT 58 AATCTTTGGTCCTAGACATAGTCCCTG 49 + ILLUMINA 0.374515269 227 FALSE ACP1 +snp_rs10489562 snp_rs10489562 snp_rs10489562 Homo sapiens hg19 chr1 96058458 96058528 + AAACCTAACTCTCTCAGTTCTGTGCTC 57 TGACGTGCAGTTCAGCAGCAGAATCT 83 + ILLUMINA 0.645112798 212 FALSE ACP1 +snp_rs109894 snp_rs109894 snp_rs109894 Homo sapiens hg19 chr5 79067989 79068064 + GAAACCAATGACAGTTCCATTTGTAGG 52 AATAGAACAATACAAGGGGTTCTTTGC 60 + ILLUMINA 0.572781688 217 FALSE ACP1 +snp_rs10914880 snp_rs10914880 snp_rs10914880 Homo sapiens hg19 chr1 34620692 34620739 + CCTGCCTGGATCCATGCATATTTGAA 57 GACTGAGGGTAGGATTAATTCAAATGT 88 + ILLUMINA 0.683500629 189 FALSE ACP1 +snp_rs11662069 snp_rs11662069 snp_rs11662069 Homo sapiens hg19 chr18 29829266 29829314 + GTATTTTTGTGTCCCCCTGAGTGG 55 AGCCAAGGTTAGAGAGAGATTTACACA 118 + ILLUMINA 0.422195942 190 FALSE ACP1 +snp_rs10996274 snp_rs10996274 snp_rs10996274 Homo sapiens hg19 chr10 66957067 66957133 + TCAAAACTGTGCATGTTGTGTAAGCC 73 GGAAATATATCCTCATCAGTCAGGACAG 72 + ILLUMINA 0.600973946 208 FALSE ACP1 +snp_rs10849968 snp_rs10849968 snp_rs10849968 Homo sapiens hg19 chr12 109694239 109694289 + CCAATTTGGGGAATGATTTCTGCAGTG 93 ACAGACACTGGCACTCTGAATTCCAT 58 + ILLUMINA 0.729389354 192 FALSE ACP1 +snp_rs10496397 snp_rs10496397 snp_rs10496397 Homo sapiens hg19 chr2 106184359 106184411 + ACATTTAGTTATAAGTCAGCTGCGTTT 39 AATGTTTTTAAAGCACTGCGTCCCCTC 53 + ILLUMINA 0.714652589 194 FALSE ACP1 +snp_rs10744116 snp_rs10744116 snp_rs10744116 Homo sapiens hg19 chr12 16476792 16476847 + GTTCCTCCTCTATCTTGTGAACTGG 74 GTGATCTTGGCAATAACTTGGAAGATT 70 + ILLUMINA 0.62372819 197 FALSE ACP1 +snp_rs10521575 snp_rs10521575 snp_rs10521575 Homo sapiens hg19 chrX 116625965 116626021 + ACAAGGCATCCAAATTATTTCATTGTG 160 CTAAGCGCAGTAAACCCAGGATGGAAT 46 + ILLUMINA 0.21337901 198 FALSE ACP1 +snp_rs11104117 snp_rs11104117 snp_rs11104117 Homo sapiens hg19 chr12 87224946 87225021 + TGGAAACCCATGAAGAGTATACCTTTT 50 CTGGGAGGAACAATACTATGTAGAGGG 34 + ILLUMINA 0.538917148 217 FALSE ACP1 +snp_rs1060912 snp_rs1060912 snp_rs1060912 Homo sapiens hg19 chr6 52389629 52389694 + TTTTTCTTCCATAGGGAGCGAGAATGG 79 TGAAAGTATTATGCCTACTTCCAACAG 76 + ILLUMINA 0.603099147 207 FALSE ACP1 +snp_rs10865643 snp_rs10865643 snp_rs10865643 Homo sapiens hg19 chr3 69099644 69099733 + GCAAATGAACAACCAAGATTATGTCTG 48 TAGTAATTCTAATTAACTGGGGCACAT 55 + ILLUMINA 0.375170888 231 FALSE ACP1 +snp_rs10153199 snp_rs10153199 snp_rs10153199 Homo sapiens hg19 chr16 860595 860640 + GGTGTGGGACAGGTCTGGGTGACTT 63 CTCGGATCTATGGAGGGTTTGCCTTT 42 + ILLUMINA 0.648977912 187 FALSE ACP1 +snp_rs1002897 snp_rs1002897 snp_rs1002897 Homo sapiens hg19 chr2 66464244 66464324 + GAGGGAGACTCCATCTCAAAAAGAAAA 1200 AGCCGCCAAATCTATATACAAACCAGG 61 + ILLUMINA 2.03E-58 222 FALSE ACP1 +snp_rs11113551 snp_rs11113551 snp_rs11113551 Homo sapiens hg19 chr12 108248223 108248301 + ACCTACTCTGCTCAGAATTGTGTTGTC 57 TTTTTCTGGGCTTGTACAAAACGTGT 48 + ILLUMINA 0.558065379 220 FALSE ACP1 +snp_rs1030356 snp_rs1030356 snp_rs1030356 Homo sapiens hg19 chr4 141826698 141826749 + GAAATGTATAAAGGGGAACTTGTTCGG 76 AAGGCACCTCCCAATCCCAGGCCTGT 106 + ILLUMINA 0.440930708 193 FALSE ACP1 +snp_rs11048057 snp_rs11048057 snp_rs11048057 Homo sapiens hg19 chr12 25623883 25623957 + GCCTAATACCCGGCTTAAGAAACAAAAC 39 GAAGAACATGAATCAGTTTGAGCTGAT 74 + ILLUMINA 0.58109513 216 FALSE ACP1 +snp_rs1156232 snp_rs1156232 snp_rs1156232 Homo sapiens hg19 chr4 126433134 126433190 + GGTGATTTCTCACAGGAGAAGTTACGT 53 AAAAAGGCAAGGCATGTTCTACCAT 46 + ILLUMINA 0.726193821 198 FALSE ACP1 +snp_rs11074037 snp_rs11074037 snp_rs11074037 Homo sapiens hg19 chr15 92604379 92604427 + AATGACGTGCCTTATACGTGTTCGGT 7 GGTGTTTAGAGGCTGACTGGCTCAT 73 + ILLUMINA 0.622865094 190 FALSE ACP1 +snp_rs10257276 snp_rs10257276 snp_rs10257276 Homo sapiens hg19 chr7 136370731 136370780 + TAAGAGCCTCACTCATTGATTTCACCC 53 AAATTATCTGGGTTACAGTCTCGGCTC 28 + ILLUMINA 0.86350649 191 FALSE ACP1 +snp_rs12588458 snp_rs12588458 snp_rs12588458 Homo sapiens hg19 chr14 67830774 67830841 + GGTTGGGTGGATCAAAGGGAATAATTG 50 AAAAGAATTATGAGAGGAGGATGCATT 84 + ILLUMINA 0.544372964 209 FALSE ACP1 +snp_rs10077711 snp_rs10077711 snp_rs10077711 Homo sapiens hg19 chr5 179587663 179587725 + AGGAAAATTGGCTCCGAATCTCAGTAG 31 AGCTTGAGAACGTCCCTGTAAAACCA 50 + ILLUMINA 0.813499927 204 FALSE ACP1 +snp_rs10279558 snp_rs10279558 snp_rs10279558 Homo sapiens hg19 chr7 114862850 114862916 + AGACAGAGAAAGAGCCTGGGCCAAAAA 219 TGGTAAGTCAAGTTAGTTTATCTGCAA 100 + ILLUMINA 0.025960892 208 FALSE ACP1 +snp_rs10508853 snp_rs10508853 snp_rs10508853 Homo sapiens hg19 chr10 37069301 37069370 + TTGCTAATAGCTGCCTTGAGTACTATG 45 AAAACTAAGGGACAGAATAGCTTCAGT 67 + ILLUMINA 0.56321583 211 FALSE ACP1 +snp_rs10793421 snp_rs10793421 snp_rs10793421 Homo sapiens hg19 chr7 54704926 54704977 + ACCCAGCTCAGGTGAACAGTTTTTCA 58 GTCTATTACCTTTTTGAGGGGGTGACA 65 + ILLUMINA 0.880437355 193 FALSE ACP1 +snp_rs10432009 snp_rs10432009 snp_rs10432009 Homo sapiens hg19 chr17 13091362 13091427 + GAGCTTCTAAGCATACTTTCAAAGGCA 43 ATTTCTAAGCCACAGACTAAAAGATTATG 149 + ILLUMINA 0.198212105 207 FALSE ACP1 +snp_rs11002643 snp_rs11002643 snp_rs11002643 Homo sapiens hg19 chr10 80478423 80478469 + TCTTTTGTTGTATGTGTAGACATGGG 126 TGTCAAGGAGCCAGCCAGGAGGAGT 135 + ILLUMINA 0.164523918 188 FALSE ACP1 +snp_rs10519010 snp_rs10519010 snp_rs10519010 Homo sapiens hg19 chr15 60551836 60551899 + CTAATCTGCACAAGTCTAGAAAAAGAGG 50 AACCTTCGAACCTGTGACATAATCTCC 43 + ILLUMINA 0.786450461 205 FALSE ACP1 +snp_rs11576172 snp_rs11576172 snp_rs11576172 Homo sapiens hg19 chr1 217324574 217324632 + TGGGTAGGTAATAGAGCCAAGTATATAG 43 AAGTTTCTGAAGCACCATATCCTGGAC 58 + ILLUMINA 0.765165215 200 FALSE ACP1 +snp_rs11133601 snp_rs11133601 snp_rs11133601 Homo sapiens hg19 chr5 10104487 10104579 + GTTCTTATAGCTTACCATTTTTACCACC 92 GATTTAAAGTGTCTCCTTGAGGCATGT 63 + ILLUMINA 0.276053492 234 FALSE ACP1 +snp_rs10215963 snp_rs10215963 snp_rs10215963 Homo sapiens hg19 chr7 26583700 26583771 + AAACATGGAGGCAAGTCAAGAAGCCA 66 AAGGCAGAGCATGCAGCTGTGATTTT 89 + ILLUMINA 0.512636745 213 FALSE ACP1 +snp_rs11265625 snp_rs11265625 snp_rs11265625 Homo sapiens hg19 chr1 153642830 153642884 + ATCATCTTAGGTTGGCTACTTTCATCC 39 ACACTTAATAACCCATAATCCTGGGCC 42 + ILLUMINA 0.833189513 196 FALSE ACP1 +snp_rs10489391 snp_rs10489391 snp_rs10489391 Homo sapiens hg19 chr1 210458767 210458832 + CGCCTTCCCAGGTAGAATTTCCTGTTT 64 GAGAACCAAGCAGCTAAGCTTGTCCTA 32 + ILLUMINA 0.766603308 207 FALSE ACP1 +snp_rs11024021 snp_rs11024021 snp_rs11024021 Homo sapiens hg19 chr11 16735412 16735495 + TTCCACTCCTGCAGAACTCAAATCAG 71 GCTAGAAAATATAACCTCCATCATGAACC 77 + ILLUMINA 0.315235357 225 FALSE ACP1 +snp_rs1034826 snp_rs1034826 snp_rs1034826 Homo sapiens hg19 chr7 108083526 108083592 + CACGGAAAGAACATATTCACCAGGAG 50 TGTCACAGTTCATTAAATGCCATACAC 86 + ILLUMINA 0.547197949 208 FALSE ACP1 +snp_rs10901226 snp_rs10901226 snp_rs10901226 Homo sapiens hg19 chr9 133483134 133483189 + GCCCCTGATCTAACTGCTGGTTTTCAT 40 TTGAACCTGATTTCCTCTCAGTGATGC 82 + ILLUMINA 0.793738181 197 FALSE ACP1 +snp_rs10997716 snp_rs10997716 snp_rs10997716 Homo sapiens hg19 chr10 53235938 53236016 + AGGTGGGTTGCATAACTCTTTGCTTTC 40 CACTGTGAAGGTGACAATAGATCCTAG 61 + ILLUMINA 0.603111114 220 FALSE ACP1 +snp_rs10739688 snp_rs10739688 snp_rs10739688 Homo sapiens hg19 chr9 129772417 129772480 + CACCGTGCTGAAGGGCTGTGAGAGTA 44 CTCTTTGTCCTTCCTCATCGCTTTCT 68 + ILLUMINA 0.58712508 205 FALSE ACP1 +snp_rs10903900 snp_rs10903900 snp_rs10903900 Homo sapiens hg19 chr10 2990174 2990231 + ATGCACAGGCCTCTAATTCAGTGCCTA 51 CTTAGTGGGCAGCAGACTTCCTAAGATA 53 + ILLUMINA 0.846296245 199 FALSE ACP1 +snp_rs10192459 snp_rs10192459 snp_rs10192459 Homo sapiens hg19 chr2 152517899 152517957 + CCTTTCAAGGAGGTTGAGCTCCACAAA 32 TTTCTCATTTTGATCCACCAGTGCTGC 54 + ILLUMINA 0.818877583 200 FALSE ACP1 +snp_rs10860066 snp_rs10860066 snp_rs10860066 Homo sapiens hg19 chr12 97073187 97073274 + ATTGGCAAGATCTAAAGTTATTTGCAT 89 CTCTTACCTTGGCTTGGTGCAGCATTT 32 + ILLUMINA 0.276871149 229 FALSE ACP1 +snp_rs10184780 snp_rs10184780 snp_rs10184780 Homo sapiens hg19 chr2 20054313 20054360 + GACATCAGGAAGAAGGGCAAGCCAA 65 AATGAGGAAACATTGCAGAGACGAACC 63 + ILLUMINA 0.757362025 189 FALSE ACP1 +snp_rs11152428 snp_rs11152428 snp_rs11152428 Homo sapiens hg19 chr18 61994612 61994684 + ATGTGTTTCCTGGGCCACTATTGCCTT 76 CAGTGTCTACCATCCGTGTAGAATCTAC 29 + ILLUMINA 0.592283456 214 FALSE ACP1 +snp_rs10925402 snp_rs10925402 snp_rs10925402 Homo sapiens hg19 chr1 237559370 237559419 + ATGGGAATCTGCATACAAATGCTATTG 70 TTGTTATCTGCCAGCAATTAGGGGC 34 + ILLUMINA 0.682003484 191 FALSE ACP1 +snp_rs10111409 snp_rs10111409 snp_rs10111409 Homo sapiens hg19 chr8 133118395 133118452 + GATAACTGTACAGTCTTTCTGTGTAGG 51 AAATGTTGCAGGAAGGGAACATCCTC 71 + ILLUMINA 0.776424516 199 FALSE ACP1 +snp_rs1011539 snp_rs1011539 snp_rs1011539 Homo sapiens hg19 chr7 14294504 14294567 + ATAGAACCCATCTGAGATTTTTCCTCT 56 CAGTAGAAGTTGGAGGAAGTCCCACAT 53 + ILLUMINA 0.706305186 205 FALSE ACP1 +snp_rs11084990 snp_rs11084990 snp_rs11084990 Homo sapiens hg19 chr19 3009141 3009191 + CTCTGCCTGTCACACTACAGATGAGA 60 CCCTCCCAGGACAAATCTGGTCCACT 53 + ILLUMINA 0.727336284 192 FALSE ACP1 +snp_rs10122609 snp_rs10122609 snp_rs10122609 Homo sapiens hg19 chr9 9283465 9283525 + CCCATCTACAAATGAACCCTTTACAGG 41 GTGTTCCTCAAAGCTATCTGCTTAGT 59 + ILLUMINA 0.766564094 202 FALSE ACP1 +snp_rs10208207 snp_rs10208207 snp_rs10208207 Homo sapiens hg19 chr2 169074864 169074941 + TAGACAAGTAACTTGTAAAGAACCACA 57 GTATTTGCGTCAACTGCTCTCCCACTT 36 + ILLUMINA 0.42061045 219 FALSE ACP1 +snp_rs10954365 snp_rs10954365 snp_rs10954365 Homo sapiens hg19 chr7 131855080 131855137 + GCACACAGCACCAAAAAGGTAGGTTT 50 GGTATGAAAAGCTGATGCACATCCCA 50 + ILLUMINA 0.828650396 199 FALSE ACP1 +snp_rs11118109 snp_rs11118109 snp_rs11118109 Homo sapiens hg19 chr1 218632844 218632891 + ATAGAATCATTAAACCACATCAATAACCC 94 TGACTTTCTGAAGAGCCACGGGGT 25 + ILLUMINA 0.36085074 189 FALSE ACP1 +snp_rs10168253 snp_rs10168253 snp_rs10168253 Homo sapiens hg19 chr2 180659495 180659545 + CCAACATCCACTTGTCCATAACTTTAGG 40 CAGAGAGAGGTTATGGGTGGAGATACA 56 + ILLUMINA 0.86511403 192 FALSE ACP1 +snp_rs11118515 snp_rs11118515 snp_rs11118515 Homo sapiens hg19 chr1 220473942 220474020 + CAGCACAATAACAGCAAGCTCTGTGT 53 AGCAGAGGAAAACCAAAGCTACGTG 73 + ILLUMINA 0.427139255 220 FALSE ACP1 +snp_rs10133359 snp_rs10133359 snp_rs10133359 Homo sapiens hg19 chr14 26719062 26719120 + AATTCAGCTACCTTAAAATGGCAAAAA 108 TCAGAGTAGTGTTTCATGTCTGAGTCC 70 + ILLUMINA 0.428648445 200 FALSE ACP1 +snp_rs1038024 snp_rs1038024 snp_rs1038024 Homo sapiens hg19 chr17 25725521 25725573 + AGAGACACCTGCCCTGGATGAGGGAAA 74 ATGTCCTCAGAGATGGTCAGCCCTCTA 62 + ILLUMINA 0.717145517 194 FALSE ACP1 +snp_rs11144978 snp_rs11144978 snp_rs11144978 Homo sapiens hg19 chr9 79225247 79225297 + GATCCACAGTGCCCCAACACAGCTTTT 50 CCTACCCTTACCCAAATGAGTGTGTT 48 + ILLUMINA 0.866855188 192 FALSE ACP1 +snp_rs10932037 snp_rs10932037 snp_rs10932037 Homo sapiens hg19 chr2 204825261 204825327 + TAGGAAACATTGCCCGGAATTGAAAGC 20 TAGCCTGAAAGCTGCAGTTACTATAGG 70 + ILLUMINA 0.699317955 208 FALSE ACP1 +snp_rs11114607 snp_rs11114607 snp_rs11114607 Homo sapiens hg19 chr12 81157358 81157422 + AAAATGTGCCAATGAGTAAACTGAGTC 89 AATTCCAGGGAGTAGACGGTAAATTGG 26 + ILLUMINA 0.55385638 206 FALSE ACP1 +snp_rs10058793 snp_rs10058793 snp_rs10058793 Homo sapiens hg19 chr5 4739730 4739790 + GTCTGAATAATTTTAACCAGTACAAATGTG 145 CTTACATCATCAGCTGAGGAGATTTCC 103 + ILLUMINA 0.150583045 202 FALSE ACP1 +snp_rs11017093 snp_rs11017093 snp_rs11017093 Homo sapiens hg19 chr10 131926021 131926095 + TAACATGTGGAGGGCTTTTCCTCTCT 50 GCATCGGTTTGTGTGAATTCTCAGCT 70 + ILLUMINA 0.598415367 216 FALSE ACP1 +snp_rs1015077 snp_rs1015077 snp_rs1015077 Homo sapiens hg19 chr6 167526427 167526503 + AGAGAATTCTTGATGCTGCAATGCATC 56 CTTCTCTAATTAAACATCTGAACCCTCTG 94 + ILLUMINA 0.373943811 218 FALSE ACP1 +snp_rs12785223 snp_rs12785223 snp_rs12785223 Homo sapiens hg19 chr10 104843932 104843991 + AGGGACCCTCTGTGATCCATTCCTAAA 66 CTTACACTTGTTCTGTGGATGGAGACA 90 + ILLUMINA 0.690399979 201 FALSE ACP1 +snp_rs10745558 snp_rs10745558 snp_rs10745558 Homo sapiens hg19 chr12 91910096 91910153 + GAGTTTAATTACCTATCCAAGGTCACCC 90 CCACCTATTTAATTCCTGTGTGTAGCT 75 + ILLUMINA 0.650857282 199 FALSE ACP1 +snp_rs10499441 snp_rs10499441 snp_rs10499441 Homo sapiens hg19 chr7 14505603 14505683 + GCTGGTGTACACAATTATTGAGACTTTC 50 GGTTAAATAAGGCAGGAGTTGTCAGTG 67 + ILLUMINA 0.569239643 222 FALSE ACP1 +snp_rs11137287 snp_rs11137287 snp_rs11137287 Homo sapiens hg19 chr9 140382627 140382694 + CTCCTCATCCTGAGCTTCGGCCTGAA 42 TGCAGCTTTTCCTTGGGAATCCCTTT 82 + ILLUMINA 0.492813933 209 FALSE ACP1 +snp_rs10489858 snp_rs10489858 snp_rs10489858 Homo sapiens hg19 chr1 19947170 19947225 + GCTGGTCTGAACTGTTGATTCTTACTTC 47 TTAGCAATGGAGTCGGCATCATTCTTG 30 + ILLUMINA 0.843030306 197 FALSE ACP1 +snp_rs10519980 snp_rs10519980 snp_rs10519980 Homo sapiens hg19 chr4 149634927 149634994 + GGAAACTGAGAACAAGGGAGGTAAAAA 124 AAGAACGGAAACATGATGGGCAGTAAG 48 + ILLUMINA 0.403291967 209 FALSE ACP1 +snp_rs10489924 snp_rs10489924 snp_rs10489924 Homo sapiens hg19 chr1 99458893 99458959 + GCATGTTCTCTTTCACACTGGATTCAC 76 GGAAATAAAGATCTCTTTGTGAAAGACC 137 + ILLUMINA 0.284522685 208 FALSE ACP1 +snp_rs11081675 snp_rs11081675 snp_rs11081675 Homo sapiens hg19 chr18 28580599 28580647 + ATTCTCTTCTCTAACACCGAACTTGT 75 CTCTTCACTTTCAAACCCTTCTTATTC 107 + ILLUMINA 0.490922718 190 FALSE ACP1 +snp_rs10183112 snp_rs10183112 snp_rs10183112 Homo sapiens hg19 chr2 38445683 38445747 + ATGTTTAGGAGGAGTCAGGGACAAATC 61 GAGAGGCTTTGCAGTTTGAGCTGTTA 73 + ILLUMINA 0.716638475 206 FALSE ACP1 +snp_rs10817727 snp_rs10817727 snp_rs10817727 Homo sapiens hg19 chr9 117979331 117979385 + ATCAGAAGCGTGAAACGGACTAATACG 35 CTGCTTGTGTAGTTAGCCTATTTCACA 54 + ILLUMINA 0.8541048 196 FALSE ACP1 +snp_rs10440685 snp_rs10440685 snp_rs10440685 Homo sapiens hg19 chr5 77182996 77183058 + ACCTAGACAATAGTGGCATACAAAGAA 44 GTCGCTATCAACTCAGATTTTCGAGTTG 34 + ILLUMINA 0.695041264 204 FALSE ACP1 +snp_rs10486239 snp_rs10486239 snp_rs10486239 Homo sapiens hg19 chr7 8584147 8584215 + ACATAGATCACAGATTCTTGAAAGACTC 66 TTTGATTTTACGGCTTTTGTATTTGTATG 180 + ILLUMINA 0.070576858 210 FALSE ACP1 +snp_rs10505770 snp_rs10505770 snp_rs10505770 Homo sapiens hg19 chr12 13025970 13026035 + TGAAAGGATCTGCTCTAATCTCTTCGC 52 ACTTCTGTGTTCAATGCATTGCTCCTC 73 + ILLUMINA 0.761045033 207 FALSE ACP1 +snp_rs10223664 snp_rs10223664 snp_rs10223664 Homo sapiens hg19 chr6 98677619 98677666 + CCTCTGAGGCCTAATGAGTTTGATATG 44 GGCAAAGTATGACCTGGACTGAAAGT 47 + ILLUMINA 0.884733962 189 FALSE ACP1 +snp_rs10490026 snp_rs10490026 snp_rs10490026 Homo sapiens hg19 chr2 210733351 210733419 + GCCTCACTTTCATAAAGGAAGTATTCA 109 CTGTAACCCATGCAGAGAACACCTCATA 54 + ILLUMINA 0.478788627 210 FALSE ACP1 +snp_rs10514527 snp_rs10514527 snp_rs10514527 Homo sapiens hg19 chr16 82137560 82137626 + TGATTCATTGCTGGACACAACATCACC 53 ACAAAAAGCACACACTTCCATGTTGA 91 + ILLUMINA 0.573918816 208 FALSE ACP1 +snp_rs10744146 snp_rs10744146 snp_rs10744146 Homo sapiens hg19 chr12 17212795 17212852 + GTTGTTTCTAAGGGTACTTCACTGAGG 36 TGCAAGGTCGTGAACAAGGGTGAGATT 40 + ILLUMINA 0.864419706 199 FALSE ACP1 +snp_rs10845745 snp_rs10845745 snp_rs10845745 Homo sapiens hg19 chr12 13466271 13466320 + TGAATTCTCAACACTAGAAGGAGAGCC 48 CAGGGCAAAGCTGTTTTTGACACAAC 77 + ILLUMINA 0.846311749 191 FALSE ACP1 +snp_rs1032886 snp_rs1032886 snp_rs1032886 Homo sapiens hg19 chr12 44528973 44529031 + CTCCAACAATCACTGGGTTATTTTCTC 47 CAGGCACTGAGTGATAATCCAAGATGG 47 + ILLUMINA 0.863052801 200 FALSE ACP1 +snp_rs10487449 snp_rs10487449 snp_rs10487449 Homo sapiens hg19 chr7 126071986 126072057 + ATCTGGTCTTGTGATGTGCATGGGTA 47 GAAATGCTGACATCAACAACCAAATCG 76 + ILLUMINA 0.573763678 213 FALSE ACP1 +snp_rs10813205 snp_rs10813205 snp_rs10813205 Homo sapiens hg19 chr9 29943550 29943631 + AGAACAGTGATGTGGTTATATCTAAATTG 71 GGAGGTTGGGGGCAGTTAAAACTCTTT 50 + ILLUMINA 0.408130054 223 FALSE ACP1 +snp_rs1003346 snp_rs1003346 snp_rs1003346 Homo sapiens hg19 chr9 111815247 111815310 + TTAGATTGGTAGTCTCCAACAACAAAA 32 CACAATAGCAAGGCCCATGAAACTCT 47 + ILLUMINA 0.650790299 205 FALSE ACP1 +snp_rs11185125 snp_rs11185125 snp_rs11185125 Homo sapiens hg19 chr1 108061566 108061615 + GCCATCTTTCTGGCATGATCTCCCATTA 54 TTCTCCAGTTAAGTCCTACAGATTTTT 86 + ILLUMINA 0.624482576 191 FALSE ACP1 +snp_rs11073674 snp_rs11073674 snp_rs11073674 Homo sapiens hg19 chr15 87361895 87361952 + AGAGAACTAATATGGGAGCATATCACC 43 GTAATTTTGGAACCAGACACCAATGGG 60 + ILLUMINA 0.823405187 199 FALSE ACP1 +snp_rs10187631 snp_rs10187631 snp_rs10187631 Homo sapiens hg19 chr2 120343750 120343817 + GATGGGGTGAGGGCTCAGAAGGTAT 79 CCCAGCACTGCACAGGATGTAGAATTA 64 + ILLUMINA 0.550731548 209 FALSE ACP1 +snp_rs11125812 snp_rs11125812 snp_rs11125812 Homo sapiens hg19 chr2 59989528 59989602 + CAGGGTAATAAGAAAACCCATTGCAGA 68 CAGTTTTTGACTTTGATTTCCGAGTCC 66 + ILLUMINA 0.654042033 216 FALSE ACP1 +snp_rs10837327 snp_rs10837327 snp_rs10837327 Homo sapiens hg19 chr11 40082709 40082775 + ACTGAAAGAGATAGAATCCTTGCCT 72 AAGCATGCTCTGAATTCTTCTTAGGT 87 + ILLUMINA 0.477712155 208 FALSE ACP1 +snp_rs10937470 snp_rs10937470 snp_rs10937470 Homo sapiens hg19 chr3 191000726 191000784 + GAATTTAATTAATTCAAAGCTGGCAAATG 167 CCCAAAAGACTTTGGATGTATCCACTC 59 + ILLUMINA 0.128492085 200 FALSE ACP1 +snp_rs10510060 snp_rs10510060 snp_rs10510060 Homo sapiens hg19 chr10 121863392 121863443 + TCTTAGTTGCTGTGAGGCTCTAGACA 48 GCTCCTCCCAGCTTGAAGTAGCATGAA 55 + ILLUMINA 0.841175985 193 FALSE ACP1 +snp_rs10871565 snp_rs10871565 snp_rs10871565 Homo sapiens hg19 chr18 75698271 75698320 + AACTTTCTATCTGTCTGCCAATTACCT 76 ATTTCCCCTCACGAAAATTAACATCAG 59 + ILLUMINA 0.678949414 191 FALSE ACP1 +snp_rs10950049 snp_rs10950049 snp_rs10950049 Homo sapiens hg19 chr7 66230777 66230827 + CGACTTAGTCCCATTTCCAAAACTCG 56 TGCTAGGCAGACTTCCCAAACTATGT 51 + ILLUMINA 0.853960602 192 FALSE ACP1 +snp_rs10816943 snp_rs10816943 snp_rs10816943 Homo sapiens hg19 chr9 112983736 112983790 + TTTCGGCATTTAATTTGGCCCTTTCTG 48 TGGGTTCTCTGGATAGAGACAGACCT 72 + ILLUMINA 0.816934363 196 FALSE ACP1 +snp_rs10512393 snp_rs10512393 snp_rs10512393 Homo sapiens hg19 chr9 112153077 112153128 + TTTTGGCTTATATGTACAGAGGAGGTT 72 CAGAACAAGTCTGGTCCCATCTTCTGT 52 + ILLUMINA 0.771009234 193 FALSE ACP1 +snp_rs10511942 snp_rs10511942 snp_rs10511942 Homo sapiens hg19 chr9 37702789 37702848 + GGTGGTGGGGAATTATTAGGAGGAGAA 42 TGTTTGGTTTATCTATTCCCTATCGGG 54 + ILLUMINA 0.832865527 201 FALSE ACP1 +snp_rs10240790 snp_rs10240790 snp_rs10240790 Homo sapiens hg19 chr7 89880864 89880915 + GGTTGTTGGCCAGAGTTATTTTGTCAC 54 CACACCTAGCACAATTCCTGAAACA 183 + ILLUMINA 0.140378825 193 FALSE ACP1 +snp_rs1147199 snp_rs1147199 snp_rs1147199 Homo sapiens hg19 chr9 87275809 87275872 + TATCAGCCTTTGGTTCCATGTGACCT 55 GTGAACATGCTTGTAGATTCTGTTCCT 62 + ILLUMINA 0.769709012 205 FALSE ACP1 +snp_rs1058326 snp_rs1058326 snp_rs1058326 Homo sapiens hg19 chr9 27446989 27447063 + GAGCATCCCATTTATTAAGGGGAAAAT 61 GAATCACTTTCCACACATGGGGGTGTA 42 + ILLUMINA 0.611393781 216 FALSE ACP1 +snp_rs10484820 snp_rs10484820 snp_rs10484820 Homo sapiens hg19 chr6 139858182 139858274 + CTTGATGGGCTTCTTCTGGGAAAACA 64 TGCTGGTCCAAGGTGCCTCTTGCTGTT 47 + ILLUMINA 0.344041341 234 FALSE ACP1 +snp_rs10829531 snp_rs10829531 snp_rs10829531 Homo sapiens hg19 chr10 130761863 130761919 + CAGGTCTCGAAAAGGAATTTGGGGGAA 75 GACCAGAAGGATGAAACCAAGCCAAT 73 + ILLUMINA 0.810076622 198 FALSE ACP1 +snp_rs10835211 snp_rs10835211 snp_rs10835211 Homo sapiens hg19 chr11 27701279 27701333 + GGCCAACTTTGCATGGTTAATCATTTAG 54 AGCTGAAAGTCAGAACCAGCTGTGTT 72 + ILLUMINA 0.755395475 196 FALSE ACP1 +snp_rs10160742 snp_rs10160742 snp_rs10160742 Homo sapiens hg19 chr11 115239304 115239365 + ACATGAGAGCCTTTGTAAGAACCTGAA 55 TGACTCTGAGACTAAAAACACTACTAC 70 + ILLUMINA 0.659815518 203 FALSE ACP1 +snp_rs10512461 snp_rs10512461 snp_rs10512461 Homo sapiens hg19 chr17 32475304 32475365 + TTTAGGAACTTGTGCAGTAGCTTCAGT 41 CCCAAACGGAGGCTGACATTATGGAAA 80 + ILLUMINA 0.70048694 203 FALSE ACP1 +snp_rs10869031 snp_rs10869031 snp_rs10869031 Homo sapiens hg19 chr9 74130207 74130257 + TTCCTTGAAGCCCTACAAGTGCAGCAT 48 GTTGGGCATCAGCATAGTCAATAGAGG 49 + ILLUMINA 0.894520192 192 FALSE ACP1 +snp_rs1055010 snp_rs1055010 snp_rs1055010 Homo sapiens hg19 chr7 29551021 29551096 + GTATCACATCTGGCTTTCAATTAGCTG 66 GACTTAAGAGGAAACTGTGGGCACTT 68 + ILLUMINA 0.555126879 217 FALSE ACP1 +snp_rs10930486 snp_rs10930486 snp_rs10930486 Homo sapiens hg19 chr2 172472487 172472552 + GTGCAATCTTGTCTATTTGAGTAATGG 57 GTTGGAGGAAGGGCATAACATAGAGGT 53 + ILLUMINA 0.660436714 207 FALSE ACP1 +snp_rs1052448 snp_rs1052448 snp_rs1052448 Homo sapiens hg19 chr9 18927931 18928009 + TAGCCGGTGATTAAATGTCATTTTCCC 58 GCTAACACTTCCAACTCCCTCTGGTT 60 + ILLUMINA 0.510605867 220 FALSE ACP1 +snp_rs10488735 snp_rs10488735 snp_rs10488735 Homo sapiens hg19 chr11 34438475 34438526 + TCTGACTTGGTGCAGATAGACTTCAAG 44 GCAAGTAAAGGGAACACATGTGGACA 75 + ILLUMINA 0.883724256 193 FALSE ACP1 +snp_rs10255854 snp_rs10255854 snp_rs10255854 Homo sapiens hg19 chr7 38959746 38959822 + GCATACCCAGAAGAACCCAAGAAAGA 54 CCCCCACCTTTACCCCAATGCCCACT 35 + ILLUMINA 0.46651904 218 FALSE ACP1 +snp_rs10961084 snp_rs10961084 snp_rs10961084 Homo sapiens hg19 chr9 13484950 13485006 + GGGGAAGAACACATTCTATACACTTGA 62 GACCAAACAGACTTAACTGCAGGCCT 53 + ILLUMINA 0.803983292 198 FALSE ACP1 +snp_rs10189774 snp_rs10189774 snp_rs10189774 Homo sapiens hg19 chr2 171375418 171375468 + CTTCAGGTTGAATTAAAGTTCAGTGGA 62 ACAGTTAATCCTAGCCACATCATCACA 60 + ILLUMINA 0.76321132 192 FALSE ACP1 +snp_rs10893306 snp_rs10893306 snp_rs10893306 Homo sapiens hg19 chr11 124813437 124813483 + TCCTACCAAAGAGGGAGGCTCAGAAAT 70 GGATCCCTGTCTAGGAGCTGAAATAT 72 + ILLUMINA 0.812343212 188 FALSE ACP1 +snp_rs1106944 snp_rs1106944 snp_rs1106944 Homo sapiens hg19 chr11 126008190 126008251 + GAACTCAGTTCACAGGAACACATATGA 67 GCCCTAACAAGTAAGTCCTCCTTGATC 37 + ILLUMINA 0.775830757 203 FALSE ACP1 +snp_rs1055352 snp_rs1055352 snp_rs1055352 Homo sapiens hg19 chr9 128910339 128910385 + AGAAAGCTAACTTAGAACCACTCCTTGG 42 CTTCGGGCACCTTGTTGGTTTGCA 24 + ILLUMINA 0.594162219 188 FALSE ACP1 +snp_rs10141526 snp_rs10141526 snp_rs10141526 Homo sapiens hg19 chr14 62303171 62303231 + GCAGTCCATTCACTTGAAAGGCATTTG 42 TTTCTACTCCACCTCCCATTGATTTGC 69 + ILLUMINA 0.803812655 202 FALSE ACP1 +snp_rs10094093 snp_rs10094093 snp_rs10094093 Homo sapiens hg19 chr8 4505832 4505882 + CTTTGCCCACTTTTTGATGGGGTTGT 1200 CTCAGCCATGAGTCTTGGGGCTCAGT 40 + ILLUMINA 2.67E-58 192 FALSE ACP1 +snp_rs11009888 snp_rs11009888 snp_rs11009888 Homo sapiens hg19 chr10 35008018 35008068 + GGAAACAGCCTAGAAACAATACACTCC 75 TAGTGCTCGAATCCTAACCTTCATGTC 39 + ILLUMINA 0.841622465 192 FALSE ACP1 +snp_rs11082351 snp_rs11082351 snp_rs11082351 Homo sapiens hg19 chr18 41484259 41484312 + ACTTTTGTCTACTTGACCCATCAAGAC 53 TCTGACTACATAGGCTTGTATGAAAAT 70 + ILLUMINA 0.682308703 195 FALSE ACP1 +snp_rs1113272 snp_rs1113272 snp_rs1113272 Homo sapiens hg19 chr4 165646689 165646762 + TTCCTTATGCATTGCAGGCTGGACAA 60 AAAACCCAAATTTCAGGAGCACATCAT 80 + ILLUMINA 0.570563977 215 FALSE ACP1 +snp_rs10250461 snp_rs10250461 snp_rs10250461 Homo sapiens hg19 chr7 22289272 22289337 + TGACTCTCCACCAAACAAAGCTTGGT 55 AGCTCATTCCCTAACTCTGCGGGTCATA 21 + ILLUMINA 0.676202224 207 FALSE ACP1 +snp_rs11143230 snp_rs11143230 snp_rs11143230 Homo sapiens hg19 chr9 74887624 74887687 + CACATACATGATTCAAACCACACAGCT 67 GAATCTCAGGTTTGGAAGGGCACTCTA 66 + ILLUMINA 0.709387958 205 FALSE ACP1 +snp_rs10520689 snp_rs10520689 snp_rs10520689 Homo sapiens hg19 chr15 90950279 90950338 + GGACTAATCAGAGGCTTCCTGAAATTG 61 AATCAGTGGGTGTTGGTTGTCCATTAG 44 + ILLUMINA 0.842056616 201 FALSE ACP1 +snp_rs11079784 snp_rs11079784 snp_rs11079784 Homo sapiens hg19 chr17 45702187 45702248 + GATTTTCCTGCACTCTGTCCATGTCT 50 TCCCTATCATAAGTCATACACCCATTT 25 + ILLUMINA 0.65022705 203 FALSE ACP1 +snp_rs11632663 snp_rs11632663 snp_rs11632663 Homo sapiens hg19 chr15 27564707 27564752 + TGTGATACGGCAGTTGAAGACATAGAG 18 GGCGTGGGCAGAGCACAAATGGGAT 45 + ILLUMINA 0.615586207 187 FALSE ACP1 +snp_rs10079889 snp_rs10079889 snp_rs10079889 Homo sapiens hg19 chr5 32975406 32975462 + CCCTCCTAACACTTTTCTGCTGCAGAA 59 GGCAGTACTTACAAAGTTAGACTTTGT 73 + ILLUMINA 0.745322966 198 FALSE ACP1 +snp_rs10504373 snp_rs10504373 snp_rs10504373 Homo sapiens hg19 chr8 65107845 65107907 + ATGACAGTTTGGTTTAAATAATATGCAAC 191 GGTTTCCTTTCTTAAGTCAGCATACAT 76 + ILLUMINA 0.056308824 204 FALSE ACP1 +snp_rs1160382 snp_rs1160382 snp_rs1160382 Homo sapiens hg19 chr7 149279913 149279967 + CTTTTGTCCTCAGGAATGTCAAACACC 81 ACTCTACTCACTGCAGCTCTCAAGGT 78 + ILLUMINA 0.708279308 196 FALSE ACP1 +snp_rs10887788 snp_rs10887788 snp_rs10887788 Homo sapiens hg19 chr10 89898673 89898732 + GAGAAGGTAAGTTTACAACAGAATGGA 50 CTAGCTCAGTGGTCCTTACACTTAAAC 68 + ILLUMINA 0.747188108 201 FALSE ACP1 +snp_rs10257539 snp_rs10257539 snp_rs10257539 Homo sapiens hg19 chr7 135439817 135439884 + GATCTCTTCTGCATTGGGTTCTCTGCT 59 CCCTCTTTGGTTGACTTCATTCATGG 83 + ILLUMINA 0.630070627 209 FALSE ACP1 +snp_rs11002633 snp_rs11002633 snp_rs11002633 Homo sapiens hg19 chr10 80447690 80447755 + GGTGCAGTCAGTAAAGCATGTGTGCTA 32 TGTGTGCATACATACAAGGGTGTGTG 67 + ILLUMINA 0.679364651 207 FALSE ACP1 +snp_rs1058932 snp_rs1058932 snp_rs1058932 Homo sapiens hg19 chr10 96796783 96796829 + TATTTGTGCAGTGACCTGAACAACTC 71 GGCTAGCATTCTTCAGACAGGGATGAA 74 + ILLUMINA 0.785343458 188 FALSE ACP1 +snp_rs11063356 snp_rs11063356 snp_rs11063356 Homo sapiens hg19 chr12 4938515 4938572 + AAAGCATGTCTGTACTTACCGTCTGAG 28 TTGCCAGGACCCCTTGAAATTTTG 68 + ILLUMINA 0.590490431 199 FALSE ACP1 +snp_rs1016726 snp_rs1016726 snp_rs1016726 Homo sapiens hg19 chr7 29356325 29356372 + GTTTTCAGGTAGAGTTGAATGTAGCT 57 GTCCAGATAATCTTGGTATAGTCTCCT 36 + ILLUMINA 0.777651511 189 FALSE ACP1 +snp_rs10875815 snp_rs10875815 snp_rs10875815 Homo sapiens hg19 chr12 48834246 48834297 + GACCATGATAATTTTAGTCCACATGCC 57 TACCATTTCTACAGCATTATTAGGGCC 59 + ILLUMINA 0.850910101 193 FALSE ACP1 +snp_rs10957982 snp_rs10957982 snp_rs10957982 Homo sapiens hg19 chr8 81455678 81455739 + GGTGTTTCTCCCAGCTGGTAAAGAGAA 57 GATTTTCAAAGAGGGCATCAGCATCAC 83 + ILLUMINA 0.785543235 203 FALSE ACP1 +snp_rs1258540 snp_rs1258540 snp_rs1258540 Homo sapiens hg19 chr7 63109190 63109244 + ATGTTCAAACAGAGTGGCCTGTTCAG 48 TGAGGATGTCAACTGAGGAGGGGCAT 53 + ILLUMINA 0.784289176 196 FALSE ACP1 +snp_rs10087078 snp_rs10087078 snp_rs10087078 Homo sapiens hg19 chr8 8930658 8930710 + GAACAAATGCATAATCCTTCATCTGGC 68 ACCACCACATAGTAGCATTAATCTGTC 63 + ILLUMINA 0.796318253 194 FALSE ACP1 +snp_rs1050190 snp_rs1050190 snp_rs1050190 Homo sapiens hg19 chr3 141644727 141644782 + CATGACATTGGGTTACATCATAACGTGC 60 GTGGTTTAATTGCCAAGTGTCTAAAGC 63 + ILLUMINA 0.801391454 197 FALSE ACP1 + +[Targets] +TargetA TargetB Target Number Chromosome Start Position End Position Probe Strand Sequence Species Build ID +snp_rs10138962 snp_rs10138962 1 chr14 104995748 104995938 - CCACCACATCCAGCCTCTACTAATGTCATTTGTAGCCTTTGTAGCACCCTTTCCCTCTCAAACTTGAGCACTTTTTAGAGCAAGAGTTTGCTATGGACAACTATGCTGGTGATGCAGGACAGGCAAGCCGCAAAGTGGGGCTC Homo sapiens hg19 +snp_rs1149580 snp_rs1149580 1 chr11 76549360 76549559 - GCCAAGCACAAAGCAGCCACCGGCAAAGCTTTTTTAAAGAGAAGAACAGACACATTGAGTTTGCACATTTGAAGCCAGGGCCAGAACTTATTTCCTGCCACCCTGATGGTAACAAAGATGCATTTTGCACTGTGCTGGGCTGTCAG Homo sapiens hg19 +snp_rs10988298 snp_rs10988298 1 chr9 132042345 132042541 - ACCTGGGATGTATAGATGAAATTTGTATAGGTGGTCGCAGTTATTACTATTATTATTATTATTTACAGACAGGATCTTGCTCTGTCACCCAAGCTGGAGGGCAGTGGCACCATCACAGCTCACTGCAGCCTCAACCTCCTGGG Homo sapiens hg19 +snp_rs10086550 snp_rs10086550 1 chr8 143362875 143363074 - GGGTTGCCCTTGGCTTCCCTAGAGAGGTCCTCACCATGAGGTCTAAAAGCTCTGGGTCCCCTTAACCCTGACCCTAACCCTGGGGTGACTGTGTCCAGTTCTGACTCCATGCGCTGTGGCCTCCTCTGCTTGTGGAGAGCCAGAGTCTCTC Homo sapiens hg19 +snp_rs10409978 snp_rs10409978 1 chr19 57796523 57796716 - AGGGAAGCCAGCACCAGACAACCAGTATTAGTGCCACAGGGGGGCCTGGCTGCAAATCCTGCCTTTGGGTTCTACAAAACATCCCATTTCCTGGTAACACATCCCTCTCCTTTGGCTGTGACCAAAAGCAAACTATATTT Homo sapiens hg19 +snp_rs1060493 snp_rs1060493 1 chr15 31516299 31516546 - GCCCTCTCCCAGAGCCGGTGGCCTGCGTGCCAGGTCCCCGACAAATGCTGGCTCCATGGCAGCTGCGATGACTTCCCTCGAGAAGTGCCAGTCCGCAGGGCAATCTCGAGGTCCTCGTGCGGGTGACCAGCTGCGGCACGGCCAGCACGGCACAGGGAGGGAGGGGCTGTGCTGACCCTCAGGTGTCTCGCGGGGGCCC Homo sapiens hg19 +snp_rs12777222 snp_rs12777222 1 chr10 35387802 35388000 - TTTCTGTGAATTAGCTTCCCTCCAGACTTACCACATTTGACTTGTTCGCTTTCTTTGTTCCTATCTTCTCAAATGAGATGGCCTATATTACTTATTTAATTTATTTATTTCGAGACAGAGTCTTGCTTTGTTGCCCAGGCTGGA Homo sapiens hg19 +snp_rs12563211 snp_rs12563211 1 chr1 34486048 34486289 - AAAAATCAGTCTGGTTCCAAAGCCCACACTCTCCACCGTGTTCCTGCTGAAAATAAGCCCTGCACAGTTCTCCAGGCCTGCCCCACTCGCCTACCCCTACCCCACAGCAGGAGAGGCCTGGGAGAGTCGGGTGGGCCAGCAGCATGACGCTGGGGCATCTCCTTGAGCCTGTGGTCCCCAGCCCTGGCC Homo sapiens hg19 +snp_rs10843013 snp_rs10843013 1 chr12 28025030 28025244 - TTCAAGTACTTCTGTGCTAGTTAAAACTGGTACTGCTCTATCCAACAACACTAAGTACAAAATCTTACCGCTTTTGTCAAAGTGAAAAATGTTTCCAGGAAAAAAGAAAAAAGCCTTTTAAGTTTGGATGAACCTTTATTTCTAATTATATGGCTTTCAAA Homo sapiens hg19 +snp_rs12678837 snp_rs12678837 1 chr8 22950234 22950426 - GGAAGGGTTGACGGAGAAAAAGTGAAGGTCCGCCCAGGGTTGGAGGAAGCCACAGGAGAGGGACCATAGGACTCCCCCAGAACCAGGACTTCCCCAGAAACCAGGGCCAGTTCACCACTCAGGGACCCACTGCCTCTTCCC Homo sapiens hg19 +snp_rs10954737 snp_rs10954737 1 chr7 83532864 83533108 - ATTTAAAGATCTCCCTCCCAATGGGAGATGCAGACATACCCATTTATTATCACAGGCATCCACAGTGTAGTTGTTCAACCAAACACACACACACACACGCACACACACATTTACATACACCCTTTCCAAGAGAAAAAATACTAATTTTTAAAGACAATGTAATTTTAATACAAAATGAAAAAGAAGCAAATA Homo sapiens hg19 +snp_rs11100509 snp_rs11100509 1 chr4 164478714 164478945 - ATAAATAATAATCATAATAGTAAATAAGTGGGAATGAAGGATATAGGCAAAAGAAAAGCAAGGCTAACCCATTTTTATTAGGTTTCCAAAGAGAGAGGAAAGAAAAACGACAGGCTATTAAAGAACTTTTAAATGAGTTCCTTTCATGTTCAGTTCTCACTCTTGAGCTTTAGGAA Homo sapiens hg19 +snp_rs12636227 snp_rs12636227 1 chr3 65065315 65065552 - TATTGCACAGTTTTATATAGTATGATGATTTTCAACAATGCCCGTATCGCTTTATAGCAGAACTGACTTTATGTTGAAGCACCCTGTGGCTGGCAACAGCAGGGAGCTATTACCACTCTTAGGTCTGAAGGAGGAGAGCAGAGAAGATGTCATGGGAATCCTGAGGGGGAGAGGGGCCCTGCAGG Homo sapiens hg19 +snp_rs10038337 snp_rs10038337 1 chr5 11512269 11512495 - TTAGGAGAATTCCAGCAGCAATGTGTAGAGACGGATTATAGAGAAGCAGGACTAACCGCACAATTTATAGGATTTGAGGACTGAACCAGTCATACAATTTGCAGGGTCTAGTTCAAAATGAATATTGTGGAGCCCTTTGTTCAAAAATATTAGGAATTTTAAGATGGCAACAG Homo sapiens hg19 +snp_rs10509415 snp_rs10509415 1 chr10 82472909 82473133 - TATGGAAAACATACCTATTTTTAGGTGATATCTTGTGTATTTTTTAAGTTGTTTTACGCACATTATAGAAACCCTTCCCATTTAACACCTTAAAAAATAACTGGGTTTGCAAAATTTCCTGATGAAATGTGTATAATTAAATGCACTTGTGAACACTGTGATTACGGTA Homo sapiens hg19 +snp_rs10757399 snp_rs10757399 1 chr9 23186299 23186491 - TTTATATGACAGGCAATAGACTGAAGTATTTAGGGGATTTTAGCTGTAACGTCTTAGACTGAGGAACCATGCAAAGGTAGCAGGTTCCTCCTGAATGAAGCAAGGAGGAGCTAAAGCCAGTTACAAAGGGTGAAAGTA Homo sapiens hg19 +snp_rs10919337 snp_rs10919337 1 chr1 170216839 170217040 - ACTGTAGTTTCTACAAGAGACTGGGTGAAGCACACTTTTCAATTTTCCAACACTCTTCAAATATGTGTTCCACCCACTAGACCCAAGCTCCTCAACTTTCTTGTTCATCTCTGAATCTCCTGCTCCTTTTCCACATTTTATTCTCATA Homo sapiens hg19 +snp_rs11205541 snp_rs11205541 1 chr1 49254244 49254474 - TAAATGAATGAACAAATAAGACAGTCTTAAAGGAGTTAAGAATCTTGCCTACATTTTCACAGTTAGTGTCCCAGAAGAATTAGGACATAAGGCAGGGCATCACAGAAAAATTCATGCAAGGAGACAAAAAGAGAACCCAGAAATGGAAACAGAAAGGCATAACATAGTTCATCCTTT Homo sapiens hg19 +snp_rs10819072 snp_rs10819072 1 chr9 101361434 101361623 - ATTCCAACAAAATGTGCTAGAAGCCCACATATAAAATCTCCAGAAGGGAACCCTTCTGGTTAAATGGTGGTGGGGACTCAGAGCCTTGCCCAGTAGGGTCATGCCATGTCAGTCTTTCTTCAAGAGGCCTCCTGAGG Homo sapiens hg19 +snp_rs1078814 snp_rs1078814 1 chr3 193732876 193733071 - TCAGGGATGGAGAAAGAGAATTCAGATCAGGTGAATCCCTGAGTGGTGAGCCTCAGCCACGGCTTCATCTTGACAGACATTTGCCCTCTAGAAACAGACTTAAGGTCAATCCCTTTGCCAAGAAGTCAAGAAACTGCCTTCT Homo sapiens hg19 +snp_rs10487657 snp_rs10487657 1 chr7 82712960 82713214 - ATTAGCTCCTTTAAAAGATATATCAAGAAAATACATCGCCACTGGAGGAATTTCAAGAATCTGTTCCAATAGTTGCAAATATGTTTGAGTGGGCAGGGTCATCACTAGTACTGTCTGAAGTCATGACAGCAACCTGAATTTCTGCTTTTTCTACATGTAGACTTAGGGATATACTTTTTACAATTTTTAAAACTTATT Homo sapiens hg19 +snp_rs10930331 snp_rs10930331 1 chr2 151750485 151750677 - CAAACTAACAGCCAGGTGCTGAAATTTTTATTTGCCTTAAAATATAAATACCAGTCTTTCTTGCTGTTGCCATTTTTCAAGAAACATACTCTATGACATATCCAATTTGGGGATGCATAATTTTCACCTGCAGGTATAT Homo sapiens hg19 +snp_rs11075329 snp_rs11075329 1 chr16 17123680 17123910 - TTATTGATGACATTTGTTGAATAAATGGCTCAAAACCCGAATTTACTCCAGTTAGCACTCAGTGCTATCATTTGTGCAATGTGGTATCAAAGTGAAGTCTCCTTTAGCCTAGGTTCCAAAGTGACTGATGAGAAAACTCCAAATAGTCAGTGTTAGAAATACAGTAAGAGTAAGAAAT Homo sapiens hg19 +snp_rs10050438 snp_rs10050438 1 chr5 10138985 10139198 - GCCCACAGACGTGGAAACTGGGACACAGTGATTTAAACTCCACCTGAGGATGTGATCCAGGAGAGTGTGGAGCAAGGAGGTCTTTCTGTCTAGTTTATGGCTTCCCTCGCTGAGTGGCGCTGCCTCTGCCCTTGGCCTTGCTGAGATTTTATAGCTGGCAC Homo sapiens hg19 +snp_rs10425564 snp_rs10425564 1 chr19 57312827 57313043 - TCTGTTTCACTGAGGAGAATATTAAAAGGGACTGGACGTCTGCCCAGTTGAGGTCATGGGTCTGAAACTATTCTGAATGAGGTTTTGAAACCCCTCAGGATCTTCCCTTAGTCCTTTAGAATGAGACTTTCCGTTATAAAGCTCTGAAGTTGTGAAGGGAAAAT Homo sapiens hg19 +snp_rs11266838 snp_rs11266838 1 chr7 126792683 126792902 - ATTATTTTTATTCATGGTTTTACCTTTTGGTAAATTCCTTTGGTGATCTTTAGATGGTTTTCTCCAAGTGTCATCAGATGCATCTCCAATTTAAAGAAATAATCTCTGTATCATAATACCTACACTCTTGTATAAAGAGAGCTCAAAACAAATTGGCAAAGGAAGAG Homo sapiens hg19 +snp_rs10870311 snp_rs10870311 1 chr10 134290364 134290563 - CTGCTCCTGTGACCGCTGCAGAGTGGGTAACAGGAGGGAGTTGATAGAAGCCCTCAACCCAAGTGCCCCCAGCTGATGAGCACCCCAGCGGCATCTCTGACCCGGGCCGGGAGCCCTGGCTTTCCAAGCACATCACAAGCTAGGCCACTG Homo sapiens hg19 +snp_rs10993058 snp_rs10993058 1 chr9 96872990 96873207 - CTAAGTGTGATATACTAGAGAACATCATAGGATAATAATAGAGCTGGTTCAGCCTTTTCCAGGACAGATGTGTGATATTTTCACTAAGTTATGGACAGCACAGTGTTCTCTTAATGCCATCATAAAATTTAGTGCTAAAGGGACCTCAAGGTCCCTGAGAAGGC Homo sapiens hg19 +snp_rs10972175 snp_rs10972175 1 chr9 34625252 34625454 - CTTCCTCCAGCCATGTCTTCCCTGTTTTCCCTTGATTCAGGCAGGGGACACCTCACGTGCTCTACAGCAGGAAGGACTAGGAATAGACTGAAGGAAGGACTTCCCAAGGGGTGGGCTGGGGACTATGTGAGTTGAGGCTGTGGAGGAGGA Homo sapiens hg19 +snp_rs11582151 snp_rs11582151 1 chr1 37796448 37796646 - CAAGGCCAGCTTCATGAAGACTACCTACATCCTCCGACAGAAACATAGCTGCACACATGGAGGCCGTATTTCTGGATCAGACCCTGCTGGTTTGAGCAGACGTGACAAGAGCAAGAACCCTGGCCGAATTTTTGTTGGTGGCTCC Homo sapiens hg19 +snp_rs11085825 snp_rs11085825 1 chr19 13007286 13007515 - CGGATGCCAGAAGATGCACTGTGAGTCAAATGACTGAGCTGGTTCAGGCCCATGTGTCCCGGGCAGAGCCGGGATGAGCGAGACGGTCACCAAATGGGGGCAGTTTTCAGCACGTCAGCGAGTCCGGCTGAGTAAGAATCACCACTGTGTGGGCTCCACAGGCACAGGGAGCCGCGTCCCC Homo sapiens hg19 +snp_rs10246620 snp_rs10246620 1 chr7 43423961 43424159 - TTCTTGCTAATGTAACATCTTTTTTCCTATGGACATGCCACATGGATACTTAGGAAAAGCTCTCTAAGGTCCAAGGGTGAGCTTGCTGCCAGCCCCAGGCACACCGCCATCTTGGGGCTCTGTCTTCCTGCAGCAGCTGCCAC Homo sapiens hg19 +snp_rs11045044 snp_rs11045044 1 chr12 20257725 20257957 - AATAGAGAATGGGAAATACATTGGTTGTTTGCACATTATCCTACACTATGGTTTCAATGGTTGTCTCCTCTGAAATTTATGTTGAAGCTTAATCCCCAGCCTGGCAGTATTGAGAGGTGGGCCTTTAGGAGGTGACTGGGTCATGAGGGATGGATTAATCCATTCATAGATTAATG Homo sapiens hg19 +snp_rs10189240 snp_rs10189240 1 chr2 144484337 144484553 - ATATCTATATAGTGACCAGCCTTTGTGCTATCCAGGTTTGCCTTTTGCTATTGGCTGCAGTTAAGGCCCTTTATCAATGACAGCAAACAAAGTAGGTGGTCTTCTACTTCTTTCTTGCAGCAGGAAAAAAATAGTGACATAATTTTTCACAGCCTGAAATAAT Homo sapiens hg19 +snp_rs11008285 snp_rs11008285 1 chr10 31130832 31131040 - GAGGTATTTTGTACCATATAAAAGATTGTAAAAAGCTTGAGTAGACAGATCTTAAGTGCCGAATTCAAGGATGGAAACTACTAGGAACCACAGAAGTTGGCATTTTTGCAGGAAATGCATTTTATTTTTATTTTATATATTTTTTTCGAGTTGGAG Homo sapiens hg19 +snp_rs11139732 snp_rs11139732 1 chr9 85365353 85365570 - TATCTTTGTTATAATAATAAAGGGAACAAACATGGGTAGCCTTTTTCTCTGGCACCTTACATTTCAGACCTCAGGGGGAATATAAACATATCCATGGATTATTTTTATAATCTCAAAGGGTCAGTTTTTCATCTTCAAAGAGTCAAATAGAATGAGAAAAGTTGT Homo sapiens hg19 +snp_rs10736719 snp_rs10736719 1 chr11 61999583 61999784 - AGGTGGACTTCATCAGTGACTCAACTCTGCAGCCAACAAAGGACCCAATGTTATGCTTGCACACAGCAGGTGTGCACTAAATACAAGATAAACATATTAATATGATTGGAGTTCATTTCAGTCTGTTTTGCTGGAGTCTAGATTCTA Homo sapiens hg19 +snp_rs10891556 snp_rs10891556 1 chr11 113352608 113352823 - TCATTTATTGATTCACTCACTGGGAGGGGCAAGTACCAGCAATGAGGCTGGAAAGAGGCAAGGATGGATGTGGTGTTAGCATGATTAGAATTTATCTCAAAGGCAACAGGAAAGGCTTTGAAGGGGAGTAAGTAGGATGACATCATCAGATTTATGTTTAAGAG Homo sapiens hg19 +snp_rs10741165 snp_rs10741165 1 chr10 130610872 130611080 - AATTAGGAAGGATGTAATTATGACATTACAAAAGTTAGGCCATATCTGTTAGGAATTTACACAGTGAGCTTTGAAGCCATGGAAACTCCTAAATGAAACTTCCTGTGTTACCTGTTTCTGAGGACACTGCAAAATGTCACCAAAGCCAGAACTAA Homo sapiens hg19 +snp_rs1055273 snp_rs1055273 1 chr16 58028786 58029008 - GGGGCAGGGAGATGCCACCATGCTTCTCTGTCACCGTAAGAAGGCTGACCAGCCACGCCCACCTCCTCTGTCTGACTGAGTTCCTTCCTGTGGCCACAGGGAGGGGCTGGTCCTTCCCCTCGGTGCTGGCTCTCTGTCACAATGCCTCAAAAGACATGGAACCCAGGC Homo sapiens hg19 +snp_rs10740396 snp_rs10740396 1 chr10 74019880 74020105 - TATCTTTTTATTATCACACATGGTTATTATGGGAACTTTTCTTCAGCACTTAGTGCAGCTGATGCGTTCGATGAGGGCTGCACAATAAGGTGTGTTGCCTCCCTCGCCAGGAAGTTTTTAAGAGTGTCTGGGCCAGGAAAGAAGGTCATCAGTAGGCCTGCAGCAGCTTCCCC Homo sapiens hg19 +snp_rs10112900 snp_rs10112900 1 chr8 19646350 19646553 - ATTACATTCTCGGTATATCTGCTTTCCTATTTAAAAATTTTCTTTCTGGAACAGGATTGGAAAATAATAGAAAACAGCTCACGCAGCTGCCTTAGTTACCAAGACAACAAAATGGAGAAATAACTGGCTGGTTGGCTTTTTTCTCTTTTT Homo sapiens hg19 +snp_rs10422772 snp_rs10422772 1 chr19 9723247 9723495 - AAAAACCCTACAGTTTTCTTTTTTTGAACAATTAGAGCCAGTGGCGTAGAATTCTGGCAAAAGGGCCCATCATTCAATCTGGAAGAAATCAAGAAGTCAGGGAATAAAAACAAGGAAGAAAAATTGTAAAAATTATAATTATCAAAGTAGGCTGACATGGTAGCTCATGGCTGTAATCCCAGCACTTTGGGAGGCTG Homo sapiens hg19 +snp_rs11002468 snp_rs11002468 1 chr10 80011892 80012099 - GAGCAGCAGGACCTCCAGCCCCGGGGCAGCTGACAGTCCCCGGAGCCCCACAGAGTCCCACTGTGACCCAACCCTCGCCCCAGCCCACCTGGACAGAAGTAGTGTGGGTGCCAATCAGTTGGCAAAGCACCTCTGCTGACCTTGGCCACCCAGGG Homo sapiens hg19 +snp_rs11044070 snp_rs11044070 1 chr12 18546072 18546289 - TTTCACAGTCCAGAATAAAACTGCACCACACTGATCATTAATAATTTTATTTGAGTGGGTGAAACAGAGGAAAATGTTGCTTATTTTATGAGTGTTATTAGCTTAAATAGAAACTGAAATATAAAACAATTAGAAATCACCAGGGTTAATTTAAAAACACAAA Homo sapiens hg19 +snp_rs10139797 snp_rs10139797 1 chr14 101708446 101708648 - TCAGATGCTTCTCCCCTTGTTTCTCCCATGACTGAGCAGCCACGCATCTGGACAGGTATCCAGAACACTCCCTCCCCTCCCTTCCCCTCCCCTCTCCTCTGTCTCTCCTTCTCTCCTTCTCCCTACAGGGTGACTGTGCATGTCGGCTGCC Homo sapiens hg19 +snp_rs10825371 snp_rs10825371 1 chr10 56435198 56435416 - GACTTGTCAGAGAAGTCTTACATGAGGAACAAATTCTTAGGTCGAAATATGAAAAAGGAGAAAATGCCTAGGCAGAAATAACTAGCTAAAAATAAAGTAAAATGAAATTTGGTTATGGTAATAAATAGAGAGAGTTAAAAATTAGATCAGATTGAAAAAAAAAAAA Homo sapiens hg19 +snp_rs11017755 snp_rs11017755 1 chr10 132944018 132944222 - TTTCAGCATTTTCACAAAGGATCTTTTCCGATTAGATCTAATACATATTTTATTAGCTGCTGCGTGGGGAAAGCCCTCCTCCCAGAGCATGTGGATTCAAACGGTCTTGACTCCACTGCAGACATTTGAGAGCAGGAGCTCCCTGCCAACTTG Homo sapiens hg19 +snp_rs11134290 snp_rs11134290 1 chr5 8202376 8202573 - AAAGAAAGGAAGCATTTTCCTTTGCTGGATGGAGACTGGACCCCTAGCACAGCCCAGGGACTGCTGTCCAGGTGTACATCTCAGGGAGGCCCTGGGAGGCCTGGCTGGGCTCGGGTCCTGTGTCTCACATGAACCTGCACCATGGC Homo sapiens hg19 +snp_rs10803015 snp_rs10803015 1 chr1 242243025 242243218 - CTGCCCTTGGCATACTACCATGCTCAAGTGACAGTTTTCAGTTTCTGGAAAGGGTGAAAAACAATTACATTATTTACCAGAAATCCCAAGGAGAGGCTGGGTGTACTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCC Homo sapiens hg19 +snp_rs1038074 snp_rs1038074 1 chr5 150358789 150359005 - TTGTGGGTTGTCCACATATCGTTTTCTAAGTTTGTTCTGACTAGTTCACTTATTAATATTTTAAAAGCCTTTGTGGTCCACAGTGAACATTTATTCTCTAATAAAAATGTATTTTCTGTAATATCCTCAAGAAATATTTAGGAATCACATCTGGAATATGT Homo sapiens hg19 +snp_rs10207380 snp_rs10207380 1 chr2 241860726 241860951 - GCTTCTATTCCCACTGGCCTGTTCCCAACATCTCCCCACCCTGTGCTAGGAAGATGCCTCCCCCAAGGCCTCCCCACAGCTGTAGGGGCTCCCAGGAAGAGTAGGCTGGCTGGCAGCTCACGGATGTGCTGGGGCCCCCATCAGGTGGGGTGGACCCCAGCTCCTGCCCTCAGGGGC Homo sapiens hg19 +snp_rs10235210 snp_rs10235210 1 chr7 116003288 116003485 - TCACATGTGTCATGTGGTGGTTTGTGGAAATCAATTGTTAAGATGACTGTTAGCTAATTTTCCAGGTGAATTCCTCTTCTTGCTCTACATATGAGATAATTTTAATGTAATAGACATGTTGAGGCATAGTAGGGGGTGGTTT Homo sapiens hg19 +snp_rs10185490 snp_rs10185490 1 chr2 71166689 71166882 - GTCTCTCCCGTCAGATGTCTTAGAGCTCTGCCTCTCCCCTGTTAAGCCAGCCTGATCTTTTCTTCTAGGCTGTTTGGTTTGGACACAGCCAAAATGGGGGCTGAGCAACAGAGGTGTCCTTGACTGCAAGCCGGTCCTT Homo sapiens hg19 +snp_rs10109406 snp_rs10109406 1 chr8 72632532 72632726 - GCCAGAACACCAGTGATTTTCTGCCATAAAGTTGAAAAGTACTGTTTGGCCCAATCAATGGTGAGATGAAAGTAATATATCAATGGTAATCATGTAAATGACTTACTTGATTACATAAATTATTCAGTTAACTGAATGGAG Homo sapiens hg19 +snp_rs10095650 snp_rs10095650 1 chr8 82918215 82918451 - AGGGAAGCCACATTTCACAGTTTAAAAGTTCACATGAAAAGCAAAAGTGCAACGAAACTACCCGGAGTCTATGAGGGAACATCGCCAGATTAATAATGTGTGAAATGTAGTCAAAACCCTGCTGCCCATAGCAGGTATTTCAGCTTTTCTTAGACTGTTAAGATAATTGGAAACTTTTAAA Homo sapiens hg19 +snp_rs10840020 snp_rs10840020 1 chr11 8339720 8339943 - TCAAGTGACCCACATTTTCCAGATAGTGTAATGTGTGGCCATTGAAGCACCAACAGTTTATCACTTAACCCTTTGGATGAAAATCATCCCCAGAAGTTTCTAGATCTCCCTTTACATAAAAAAAAACCTATACCTTTATTTCTTTTTATTAAAATAATAAATATGCATTAT Homo sapiens hg19 +snp_rs10502584 snp_rs10502584 1 chr18 29797319 29797530 - GTATCTCCAAGTTAGGAAAGGCCGATAGCACAGATAACAGAGAAAGTTTAGTTCTCAGTGTCCCATGCCCGCCACCCTCCAGATTCACATCTTGGCCAAGGGCTCCTCAGAACGTCAGTATCTTCATCTAGAAAATGGAGGCAGCTACACTTAAAA Homo sapiens hg19 +snp_rs10106093 snp_rs10106093 1 chr8 29355272 29355473 - TTTATGTTAAGTTGTTGCTGTTGCGTACAAACAAGAAATTCCTTCCCTAGCAGAGAAACATATTGCCACCCCTTCAAAAGATCAGAATGACTCTAACATGAGACACATCTTGCCAGGGCTGCTGGGGACTCACAGGGCAGGAAGAACAGG Homo sapiens hg19 +snp_rs10832136 snp_rs10832136 1 chr11 13925578 13925779 - TCAATAGTAGTACACGAGTGGCAAAACCTAAAGTCTGAAACCTGTACTATTTTATAATTATCTATCATCGGAGCTCATAATGCCCTGTGAAGGGATTTTGTTGGTATTTTAAAATTTCTTTACAATTAGACCTGACTGGCTCATTGG Homo sapiens hg19 +snp_rs1028530 snp_rs1028530 1 chr14 27441005 27441195 - TGGACTATAGGTCGGTAGTGGAAGTCAATTTCCAAATATTCACAGCTTCTCAGTGTTGCACCCAAGTTTTAAACAGTAGTGTTTAATCCAGCTTGAAGTCTGCAGTTACCAGAGAAGTACCTGAGCTTCTCCCACGTT Homo sapiens hg19 +snp_rs10936922 snp_rs10936922 1 chr3 176675123 176675357 - AAAAAAAGAAAAAAAGAAGAGAGAGGACGGGTCATGAGCAGGTGCATCCTGGGATGCCTCATTACTTTAGGAAAGGCCCTTATAGGCAGAGCTGAGAACAGGAAGAGAGGCCAGACCAGAGAGAGCTGAGATGTGTGGTGGGTGGTGGGCCTGGCTCTTTATGAACAACTCTTTGCTGAAA Homo sapiens hg19 +snp_rs10184938 snp_rs10184938 1 chr2 9912848 9913056 - AATGTCCATAAGTTGGGGGTCTACGGTGTGTCCGGTCTGGGGACAGAGATGGGACCCCCCAGAGACACCGAATGCAGGATTCTTTCGACATCTCCAAGAGGTGCTGCTGTAAGACCCCCGTGTGCCCGGGAGGAAAGAGAAGCTGGTGGACTTGGGG Homo sapiens hg19 +snp_rs1028850 snp_rs1028850 1 chr13 40941330 40941524 - TTAAGAGATGGGTTTGCAATAGAAAGCCCAGGATTGAAATTCACAAATTATTTACAAATGCTTTGAAATTACAGTGCCTATAACTTAACTTCTGTGTACATAAAAGTCACCTGGAGGACTTGCAAAAAGATGCTTGAACCT Homo sapiens hg19 +snp_rs10913469 snp_rs10913469 1 chr1 177913365 177913568 - TTTATGTCCCCTAAAGGTCTGTATTTTATAATATGAAGGCAAAACCTTGCAGAGGCCTCTCTGCTGGAGGCTCCTGCCTCACTGCTGATGTTTGAACGTCCTGCCTGCCGCCCCGGCCTGTGCCTCACTCCTGCTGTCAGCTCCTTCTCCCC Homo sapiens hg19 +snp_rs10490198 snp_rs10490198 1 chr2 67121519 67121740 - TTCAAAGAACATAGCAAAGGCTTTCAGCAATATGTAACGGTGGAATGAAAAAAGGAGCACATCTGACAATTCTAGAATTCTTATTGTCTCTCATACTAGTTCACTGATGCTCAACCACAGTCTATGTTGTCTCCCAAGGGACAATTTGGCAATGTTATAAGACATTTT Homo sapiens hg19 +snp_rs1147960 snp_rs1147960 1 chr10 44971311 44971532 - TCATCCAACATTCATCGAGCACCTATGGCATACTGTGCCAAGCATGGGTTGTCCAAAAGTAACTGATGCACTTCCTTTACATGAATGTGATTAAACACTATGTAACAACTAAAAGAGATGCAGAACGAACATTTAATGATTTGGAGAAGGAATATATTCTATAGGAAAAA Homo sapiens hg19 +snp_rs10489168 snp_rs10489168 1 chr1 44727828 44728042 - AATTGAATTCTCCTGCGAGAGCTCAGATGGGCATCCAGAAGGGGGCCTTGAACTGGGCCTCTGTGAAGGATGGGGACTGTGCTGTGGAGACAAGTGTAGGCTAGCATGGGGCAGAGAGGACAAGTGTCAGAGATCAGTTGGTTAGGGTGGGGCTGGGCCCAG Homo sapiens hg19 +snp_rs11241298 snp_rs11241298 1 chr5 114282888 114283088 - TATTTCTTGCTACGAAGCATCTGGGCACAGGAAGAGTCTATTTAACCTCCTGAAGTGGACTGGGGAATGAGTCTGGTCTAAACGGATGTTCTTTGTTGGCTTCTGTTGACCTCAGCTTTTCTTGCCTGGTTTCTGGGAATTGACTTCT Homo sapiens hg19 +snp_rs10935172 snp_rs10935172 1 chr3 135275536 135275741 - CTTCAGGGCCTTTGGGTGTGATTCATTGGCTTCTGGACATCTGAACTTATATGATGGAGGTCAGTGCTATCTGAGCATGTCTTTCTCTGCTTGTGACTTTGGGGCATTCTTGACCATTAAGCATATGCTCTGGGGCCGGGGCAGACCAGGCCTGC Homo sapiens hg19 +snp_rs10746385 snp_rs10746385 1 chr1 219706253 219706467 - CACCTTCTATGCATAAAAACCCATAGACCACAGGTCAGATTTCTTGAATGTGTTGTGTGAAGGCATGTGTGTGCTTTAGGATTTTATTATTTTAAACTTCTACTTAATTATAATGTCATATATTATTCTTTAAGCTTTATATTGCAGCTAATTTTAAAAAT Homo sapiens hg19 +snp_rs10834253 snp_rs10834253 1 chr11 24001808 24002038 - TCACTCACACCCCCTCTCTCTTAACCCCTTCTTAACCGTTTCCAAGTAGGCTTCTCTTGAGAAGGGGTCATTTTTGGTGTTACTTATGGTCTCAAGATGGCCACATTTGGTTGCAGAGTTAAATAGGGCAAGAATTCTTGTTCTTGAAAATACCTCCTGTTCAATGAGAATATAATT Homo sapiens hg19 +snp_rs10068395 snp_rs10068395 1 chr5 178252212 178252426 - CTCCCTGGCCTCTGTTGGACAATCTGATGAGATGGAGGATGAAGAAGGCTGAGCCTTGTGTCCTACAAAGATCCTGAGAGCCAGAATCACAGGTGGGTCAGCTCAGTGGGAAGGAGAAGGGATTCTGGAAGCCAGTCCTTCATGGGATGCTCTCCAATAA Homo sapiens hg19 +snp_rs10482536 snp_rs10482536 1 chrX 123884032 123884243 - GTTATAAAAAGTCTCTAATTTGATTCTGTCTTCCCCCCAGAAATGATTAGCCACTCGTTTTAATGGAATACCCACAGCCATAGTCTTCATGACAACAAGACTCTGTGTAAATGGTTTCAGTTGGAAGGTGGGAAGAGGCCTTAACATCTGTGTAGCCT Homo sapiens hg19 +snp_rs10512096 snp_rs10512096 1 chr9 82730172 82730406 - CTATAAAATAGTCAATAAATAGGCAACAGATAAATTAACAGATAAAGGCATGACTTTCTTTCCAGATGAACACATTCTTTAAAAGGTGCCAAGACATGAGCAAAGAGAAAAATTTTGTTTCCAGGCACAGAGTGGCATCTGACATGTAAATGATACAGACAACAAGTGCTACAGCAATTT Homo sapiens hg19 +snp_rs10765017 snp_rs10765017 1 chr10 129168728 129168937 - GGCTATTGGCACCTATTTGAAAGATCATGGAGAGAAGGATCCCAGTAGTAGCTAATCCAAAAGCCAATTATATTTGGTTTGGAACGCATAATTTTTGTTTTGGGTGAGATTTACTATTCTTACTCTAATGCATCTATAATTTTATACATCTGTAAT Homo sapiens hg19 +snp_rs1049564 snp_rs1049564 1 chr14 20940455 20940646 - TTGGGGATTTCACCGTAGTCAAAGATCTGGGCCTGAGTTAATTTATCAGTCAGACCTCCTAATCCAGAACCACAGATTATTGCAACTTGAGGTCGGTGCTTAGTGTGAGACAGAAGCCATTCTGCAGTGTTCTTATAA Homo sapiens hg19 +snp_rs11094448 snp_rs11094448 1 chrX 147217241 147217437 - TGATGTTTGGAGGACTGTATGTCATGTTCTGCTTCCAAACCATCTACTTTACTATTGTTGTGAAATACAGATCTCTCAGACAGGAAAAAAAAAAATTGATTTGACTCAAGTTTTGCCTACTGTTTCTGATGCCCAGGAGTTTT Homo sapiens hg19 +snp_rs10852042 snp_rs10852042 1 chr15 96562980 96563173 - TATATAAAGTAGATGGTGTAGTCGGGTGTGACTTTTAAGATTACAATGAGTTCTGAACAGGTCAGAAGGATGGTAGCAGGTAACAATTGGAATTTGCACTGAGGCACATGCTTGCCTGCAGTACTACCGTGAATATGTAT Homo sapiens hg19 +snp_rs10492367 snp_rs10492367 1 chr12 28014811 28015013 - TACTTATTATTAGACCCAGAGTGCTAGAGAGAAAGTGTGACAACCAACAGCTGTCCACAGCTGGCCTTTGAAAAACAGCTTCTTGAAATTAAATGCAGCAGCTGCAAGCGCCTGGCCAGCAGCATTCTGGGAAGTCACCTGTGTCAAGG Homo sapiens hg19 +snp_rs10519420 snp_rs10519420 1 chr4 138313010 138313220 - TTCTACTTCCGTTTTTACTGATTATACATCTAACTAAGCTTCAGTGAGGTCATAATTAAATGTAATGTTGTTTTTGGTTTAAAGGGAAATCTGCAATCACAGTAATGTGTGTTCATGGAACCTGAGTGTTATCACATGAACACAGACACCTGACCCA Homo sapiens hg19 +snp_rs10278557 snp_rs10278557 1 chr7 15698880 15699077 - CACATAGCAGACACAGATATAAAATTTTCATTTTATATGCACACACCCGACTGCAAAAGCATTTGTTTTTTTACTACCACTAATTCCTGTGCTTACATATAAATATATGAAAATTGGTTGCAAAAAAGATGCAACATTAT Homo sapiens hg19 +snp_rs11017144 snp_rs11017144 1 chr10 132012809 132013003 - CACTCCCTCTTGCACTCATAAAGCATGGCTCCCAAGGTGCACAGCACACCACCTTCAGGCCCCGGAGCACGCTCTGAAGGCAGCAGAGGCAGCGGCAGCAGGCCTGTATCTTAGGATTCACCAAGTACAACTCCCCCTGG Homo sapiens hg19 +snp_rs12651141 snp_rs12651141 1 chr4 89287556 89287747 - TCTAAGAGGAGGCAGGAGCGCTGCAAGTCTCCATTGTTCTTTTGCCTTTCTCTTCTTAGACTGTCTTCTCTTTAACTCCATTGTTCTGAGTTCAAAGCCCACACTCCGTGCTTTCAGCCCTTAAGACAAATAAAAAAAT Homo sapiens hg19 +snp_rs1040247 snp_rs1040247 1 chr8 139533211 139533407 - AGTGTGAACTGTATCATGCCCCAGAGCAATCACCTTCTTAATAATAACTAGCATTTATAATGCAATTGCAACATACAGAGTGCTTCTGTAACTCTCATGATTCTCCCAACTGTGCTGTGTGGAAGGACTTGTCAAGGGTTACACA Homo sapiens hg19 +snp_rs10103493 snp_rs10103493 1 chr8 97352386 97352583 - GTGTTGAGTGAATAGGTGTTTGTGAGATTATGTGTTTCTGTGGGTGGATATGTTTGCGATTTCAGGCATCCTATTCTCATGCACACTCCTCCACCGTCAGCATACTTAACGGACCACACCAAGAAAAACACAGCTCCGTTCACT Homo sapiens hg19 +snp_rs10180924 snp_rs10180924 1 chr2 86021761 86021963 - GGGCAGGGGCAGTTGTTCGGACAGCGTGTCCAGCTCCTTGTAGGAACAGGACCTGTGAGGCTGCCAAAAGGGGCCAGGGCCTCCCGGGCAACTGCTCCCCTCAAACCTGGCTCCTGTCCAGCCCTGTTCTCAAAACCAGGGAAGGCAGCCC Homo sapiens hg19 +snp_rs10061008 snp_rs10061008 1 chr5 141744359 141744551 - TGAAGGGCAAAGTCGAAATGCAAAAACACCGTAATTAACGTTTTGTTTAGAGGCGCTTTCAGAGATTTTGAACCTTAGTCTCAGAACCATTAGACACCCTTCAGCAAACCACAGGGCTGTCCACCAGGGTGTCAGCCCCA Homo sapiens hg19 +snp_rs12570664 snp_rs12570664 1 chr10 1816144 1816340 - CACTGCCCTGTTGTGTCCTCACTCATCCGGGAAGGAGGGAGAGGCATGAGCCAGGCCAGTTACAGCATAGAATAAAGCCCAGCTGCAGCCATACCTGCGGTCGGAATTACTTCCTCACAGACCATTAGCAGAGGTGAATATATA Homo sapiens hg19 +snp_rs11017185 snp_rs11017185 1 chr10 132096004 132096235 - TGTTGATGTAGTTGTTTCTTTTTGGGGAGGGAAGTCATTTTCCAGCTAATTTGTATAGAGTTTTGGACACAAGAATCTAGGACCAAGCCACACCAGTTCTCTCCTTAATCCACTACATTTACCTTCTGTCTTAGCCATGTTTCCAGAGTCTGTCTTGCCGAGACCAGCTCGGTCAGGGAGAC Homo sapiens hg19 +snp_rs10252308 snp_rs10252308 1 chr7 148501551 148501740 - ATACATACTCAGCCTGTGCATCTGGTCTTAGTGCACAGCCCAGCTCTGATTAAACCACAATGAATTTTTCTACAACCCAGGAGGTAAAATATTGATTTTATAAAATATGAGTTCAAGTTGTCAATAGATTAAACCTTT Homo sapiens hg19 +snp_rs10490542 snp_rs10490542 1 chr2 207587156 207587383 - ATTTTATTATGGGACATTCTAGAGTGAATCTGTGCCCACTTACCAGAATTGTTTTAAGTGTATCTTTTGGGACCTGAAAACTCAGATATTTCAGCTCTCCAGGTGTGCTCATGAAGTAAAACACCTATGCTTGGAGTTCAAACATTTTTTAAAGACATGTTAAATTGATTCCTATA Homo sapiens hg19 +snp_rs10776798 snp_rs10776798 1 chr1 115862094 115862292 - ATGTATGATTTTGTCAAGTTTTAAAAACAACTGATGCTACCACCCTTGTACCCGCACTACCATTCCACTTCTCCAAAGAAATTTGCCAAAAGAAAAGGTGAGTTTTGAGTTCTACTAAGTCTGTTAGGAAGCAAGGATGAGCAGCC Homo sapiens hg19 +snp_rs10894631 snp_rs10894631 1 chr11 132829527 132829716 - GTGTGTCCTGAAGTATTCTCTCTTTCCAATTTCCTTTCTGCCTTCCAGATTTAAGGTGCCACTTCTAAATCTGAGCCTGTGTATAGTAGTATTGTATTGTGTGTAGATCCTGATATTTTCCCGAAGTCAATGTAGGTAA Homo sapiens hg19 +snp_rs10505173 snp_rs10505173 1 chr8 113486062 113486272 - CTTCAAAGGAAATCAAACGATCAGCTTTAATACTGATGAAATATGAGTGGCAGTGACAACAGGCTTCCTACTAGCTGTCGGCAACAGGCTCAGCCCTACCCTCAGAAGGCGCCCTAAAAAACCTACAGTGTAGAAGAGCACACCAGACAGTGTGCTCT Homo sapiens hg19 +snp_rs10016530 snp_rs10016530 1 chr4 183824807 183825039 - CTGAAGAAGATGCTTGACTGGTAGGTTGTGGACAGTGTGTGAGGACATGGTAGGGAGGAAGCAGAGAAGACAGGCAGAACCAGGGGTCTCCAAGACCCCTGAGTGCATTGTTGCAGGAGCGGAGACGGAAGTTCTTGCCTCAGCTTTCAGGGCCCTGGGCTGTGGGCAGGCGGATGGGCACCC Homo sapiens hg19 +snp_rs11125183 snp_rs11125183 1 chr2 49013496 49013698 - GTCTTAGCAGGTGACTAAATGGCAGAATGGCAAAAAATTAGACAATATACTTCTTCCAAGAGCCCTCATGACCTGCCAGGACCTGCCATGTCTTGTATAAGTTGATATTAAGTGCTTAATTTCAGTATAACTATAAGCTAACAAAGAAT Homo sapiens hg19 +snp_rs10113311 snp_rs10113311 1 chr8 61888301 61888507 - GTGGCTTGTGGTATCTCCATCTTATGGTCCTCCTTGACCATTTAACTTTCACATCATTTAAGTTCTGCTGGGACATGGGTTCTTTACTCCAGCACAACTAGCTCCCTCTTAAGAACAATAATTATTTCTTAAATATTATAATTAATGTGAAAGAGG Homo sapiens hg19 +snp_rs10516939 snp_rs10516939 1 chr4 94574549 94574740 - TGCAAGTTAAGAGGGTTTGTGAATGTTGTGTTGGCAATTTTCACACATACAAAATAGCACACTTCTGGGAAGTGTTTAAATATAGGTATTATAGAATGTGCCTCAATCCATGTTCTTCTTAGAAGTGTGAATTAATTTA Homo sapiens hg19 +snp_rs10790866 snp_rs10790866 1 chr11 127063081 127063299 - CAAAGCAGAAATGAGTCAAATTAAGGAAATACGCAAGCATTCCAGAGCACAGCTATAACCATTATGCCTAACCTCCCTATCACACATTACAAATCTACTAAGTGCTGTCAATTAAAAAGGGTGTAGACTTTGGATATTGGGCATAAATAACAGGATGATAAGAA Homo sapiens hg19 +snp_rs1029864 snp_rs1029864 1 chr2 107784235 107784444 - TCTACCTCTATCTATCTGCCTTCCAAGGACACAAAGGAGCCACTCTGGAAGAAGAGAATATCATCCAGAGCCTCTGCAACTTATACAAATGGTCTAGCATTTAAGAAAATTGTCTTTGCGTGCTAAGAAACATGACAAGGAGATTAAAAAAAAA Homo sapiens hg19 +snp_rs10869715 snp_rs10869715 1 chr9 78780323 78780526 - CCCTGCAAGTGGTTTCCAAATAAATTACTTTGGATGAAGCCTGGTAGAAAAGATGACCATCAAGTGTAGTATATCCTTTTGAGGAATTAACTCAGGAAATAACTTACATAATTACTGTAAGCTTTATTTCCCTTCCTCTTAAAGAGTCTA Homo sapiens hg19 +snp_rs10248924 snp_rs10248924 1 chr7 138831555 138831769 - TACTTCATTTCTCCTGCAAAGAAACAATGGAAATAGCCTCTGGAGGCATAGCTTGACAACGACAATGGAAAGCCCTTAGGTTACAGTTAATACTATTTGACCCTTCCCCTTATCTTTTCTTTTTCTTTATATTTTCTCCCTTTCCTTTTCTTTTTCTGT Homo sapiens hg19 +snp_rs10836419 snp_rs10836419 1 chr11 35580524 35580766 - TACTGTTCTATTTGAATGATAAATGAAAGGGCCACACCATGCCGCTAAGGCTGGGAGACTTGGTGATACCAGACAACAGATATTTGATGAGAATTGAAGAATTGCCCTGATTCTTTATTTCATTATACTAACATAGATATAACCAGGGTTGAGCTTTCAAATAACAGATCTCTAGGTTTCTATATTCTT Homo sapiens hg19 +snp_rs10484150 snp_rs10484150 1 chr14 83637774 83637991 - CACTGTCATATTAACTTTACCATTGCCCAGTTTTGACAGATTCCAAAAGTACTTCATTCTTTCCTTCTTCCCTGCTGAATCTGCCATTTGAAGCTTTTCACTACAAAGACTTAATTTATTGTTCCTGTCTTATCTCTATTCTCCCCTTTGCAACTTCCTATTCT Homo sapiens hg19 +snp_rs12719046 snp_rs12719046 1 chr7 51334321 51334542 - AAAAATGTTAGGTTTCTTGGTCTAGGTGTCCATAGCACTCAAAAAACATGTGGAAAAAAACTGTGTGTGGGTGCTTGTGTCGTAGAGTCCTTTCCTTCCGTCCATTTGTGGGAAACAGGGACAGCCCTTGCATATGCCATGTTATTTGTGTAGAAGTACTTGCAAGCAG Homo sapiens hg19 +snp_rs1152562 snp_rs1152562 1 chr14 56878975 56879187 - CCAAGACAGCTCGGTTCTAGTGCCTGTTCCTCTTCATGCAGCTATTGATTTACATTTTATTTTGTTATTTTTGAAGACTTCAGCAAAATTAGCAATTGAGGTGGTGAAGTATTTTTCTCCTTTGAAGCATAACTCCTCCTTTTCTTCTATACTGAAAAAAA Homo sapiens hg19 +snp_rs12679346 snp_rs12679346 1 chr8 34068300 34068513 - ACAGATTATACTTAACCTTCACCTGGACGAGGAATGGGTCCATGACCCCTAGAATCTTCTCATGCCATGGTGGACATAACTCCTTCTCAATAATATATAAATTTGAAGGACTGAATTACCACTTTGATGACTTTAAAGAATGACTGTGACTTTCTAAATT Homo sapiens hg19 +snp_rs11095604 snp_rs11095604 1 chrX 13143740 13143939 - ATGTCTACCACGGATGGAAATTTGAAGGGCAAAACAGAAGTGATTGGAGTTCTGAGCTACAGTTGCTTATAAGCAAAAAAGCACATGTCTGTATTTTAAGATGACTGTGTTTCTCTTCCAATCAACTTTCTTCAAAGCATTAATCAC Homo sapiens hg19 +snp_rs10059981 snp_rs10059981 1 chr5 3619368 3619557 - GCCTTGGAGACATAAACTTGGCTTAACGTGGAACATTCCTTCTCTGATAGGGACACTCAACTCTGGAGTGCACTGATACCTGGAAGCCTCACAGTGAAGCAGCAAGGACATTCCTGAGACTGAGAAGCCCTCACTGC Homo sapiens hg19 +snp_rs11070073 snp_rs11070073 1 chr13 94692771 94692967 - TCTGGCCACATGCTGCAACCTGAAATCATCGTTCTCAGGCTTGACCTTTCCTCTCACTTTGTTCTGGCAGCTTTCCAAAGAGGGATAGGTGGTTTTAGGGCATTTTCTTGTGTTACAAATCAAATAATATTTCATGGCTTTCA Homo sapiens hg19 +snp_rs1144171 snp_rs1144171 1 chr6 91698101 91698320 - GAAAGAGACGCAGTGCTTGTCAAACCACGTGATCCCAATATGATTGTCAGCAGTGGAATTAAACTCCCCTCAAAACAAAAACAAAAAAACACTGAACTTGAAACCAGTTAAATTAGGTTATTTAAGTTATTTTAAAGTTTTTAAAAATTATTCTTGTGAAAATGAT Homo sapiens hg19 +snp_rs1049269 snp_rs1049269 1 chr10 73819850 73820055 - CCGAAGCCCCCACACTGCCTTTCGCCCTACTGAGACTGGTCCCCTCAAAAGGTAGACAAAACAGCAGCTCCCTGTGGAGCTGAAGGGCGGCCTCAAAGTGGCTTTTTGTTAGACAAGGTTAAGGTTTCCTCATGAGCAAGGTTGCAGATCGG Homo sapiens hg19 +snp_rs10263803 snp_rs10263803 1 chr7 20437670 20437862 - TACCAAAATAGGTCCTCTTACTGGGCAGAAAACCATTCATTCATTTATTCACCCATGTATACACTCATTCAATAAATATCTATTTAATGCCTATTGTGTGGCAGGCACACACTAATTTCTTTCATTACAATCTTCAAAT Homo sapiens hg19 +snp_rs11121704 snp_rs11121704 1 chr1 11293794 11294006 - AATGCTTCAGGCACATCATCGCAGATGTTTGGAAAGGAGAAGTAGGTAGATAGTAGCATAAAATAGCTCGCCCAAAATGAGGAAAAAATGAGCTTGAAAATCTGAAACAACCTTCAAATCTCAACACATTAGAGTCACGTGAAGTCCTTTATAATGTAT Homo sapiens hg19 +snp_rs10471977 snp_rs10471977 1 chr5 55750233 55750422 - CCCCGTGGCCCTATGTTTACCATGCATTCGATTCTCGGTGTGGTCCGGGCCTTTCTCACCTCATCCATTTCACCTACCAAGAAAGGAAATGACATTCATCCGGGCTGGGGCACTATTGCGCAACAAAACAAGCCAA Homo sapiens hg19 +snp_rs1005790 snp_rs1005790 1 chr5 160174797 160174990 - CCTGGGAGCCATCAGTCTGGCTAAGGGTCTATGGTGGACTTGAGGCAAACAGGGAGAAGGATGACAGAAATGTGCCAGAAGATGAATTAGAAGAGAAAGCAAAGGGAGGACAAAGATAAAAGCAAGCTATGAGAACAAAAA Homo sapiens hg19 +snp_rs10863725 snp_rs10863725 1 chr1 208950647 208950908 - ACTTATTCATTTATCAAATGTAAATACTAAATGTTTGGTGTATATCAGACCCCAGCTGTAGGATTGAGGATAGAATAAAGAACAAAAGAGAGAAAAGGTCTTTTTCCTCTTGGGGATTATATTTCACTAAAGGAGAGTGTATTAGTATGCCATGGTGGCTGTAACAAATTACAACAAATTAGTGGCTTAAAACAACAATTTGTTCTCTC Homo sapiens hg19 +snp_rs10930259 snp_rs10930259 1 chr2 167842485 167842681 - AAATGTATGAAGTGGCGCCCTTATTTCCAAACCTCCTCTGTCAGAGGTAGAGAATACCAATGCAGCTAGGCGGTCTTGCAAAGCACGGTACTCTCTCTGGTACAACCTGGTGCAACCATTTCCTTCTGCTGTTATAGGAAATAT Homo sapiens hg19 +snp_rs10813743 snp_rs10813743 1 chr9 32109898 32110112 - TCCCAGTGCTTGCATTGGAATGGATCCTCCATTTTCCTGGTTCCATATTGCAGATTTTCAGTTTCTCTATTTTAGCATCTGACTCAACCTACTCTACACTCTGCGTCTGTGTGAAGGAAGTTGCATTTTGAAGGGAGGACAGAGTGGCTGTTATTTTAA Homo sapiens hg19 +snp_rs10906498 snp_rs10906498 1 chr10 13859244 13859448 - TCATTCTAGTTAGTCGTGTCCTGCCTGGAAGAAGCAGGCCAGGAAGTAGTCAGGACCTGATCTGGAACCCTGTAATATGCTGGGAACGTGAACAGTTCCCACTGGAATCATCCAGTGTTCTCAAGAACTCAGATCTGGGTCCTGGAGCCAC Homo sapiens hg19 +snp_rs10195834 snp_rs10195834 1 chr2 66826907 66827099 - AATATATCAAGATATGCCCACAGGAAGCTAGGCATATATTTGGAAGCTGTAATTAGAATTACTTGGTTATATATAAGAGAAAAAAGCAAGCTAACAGTGGCAAACAGAAATAAAGAGAGAGGGAGGAAGGAAGGGGAGAGAGGA Homo sapiens hg19 +snp_rs10248887 snp_rs10248887 1 chr7 23711617 23711804 - TAAAAGAAGATGAACTTTGTGTCTATGGCCACAGTAGAAGTCTCAAACTGGTCCATCCGTGAGTTATTGGATGCCACTGATCTCTGGCCTTCTGAACCAGCTCCCTGGAACAGGAGGGTCTTTACTAAATAAGAG Homo sapiens hg19 +snp_rs10135821 snp_rs10135821 1 chr14 97199737 97199936 - GCTACATTACCTTTGATTACCTTCTGGGCCTGTGCTTTCTAATGCATGGCCTTAATATCTTGGTGGGCGCCATTCCTGTTTGGCTGAGAGACTCGGTCCCCAGCCGTCTTGGCCGGATGCCTCGGGCTGTGATGCCTGGTGGGAAG Homo sapiens hg19 +snp_rs10999042 snp_rs10999042 1 chr10 71707263 71707451 - AAAATGATCACGTAGGGGCCCACAATCAGGGCAACCTAGAAAGAGCTGGACACATGGATCTTGTTGCTGGATAGCAATGCTAAGCTGGTGGCTGCCATGGGATTCAGTCTCTCCTTGCTGTGTGGAAAAATACAGGC Homo sapiens hg19 +snp_rs10036347 snp_rs10036347 1 chr5 56694491 56694710 - TTCCTCCACATTATAAACTAAATGCCAAGTCGTGACAATACATTTCCTAATGGGAAAATAGAGACTTCACAGGCGCTAGAAAAGAACGAAGGACATGAGCTGTCTTTAAAAAGAGCAAATTGACTAATGGCTTAATAAATAGGCTTTCTCTACTGAGTGAAGCAAA Homo sapiens hg19 +snp_rs10189159 snp_rs10189159 1 chr2 50714405 50714615 - GGAACCACATTAGGTCAATCAGCGTCCCCCATTGACATCACATGAATGTGGTTTTCTGTGTCCATTCTTAAAAGTGGCCCCTTTTTGGCCTTTGCAATTAATTATTTTGGTTGTTCGTAAGGACAATACAAGAAGCATATAGCATTATAATTAATAAT Homo sapiens hg19 +snp_rs10491907 snp_rs10491907 1 chr9 9963788 9964001 - ATGAAAGAAATGCTCATAAAAATGGAAATGAGGCATAATTTTCCATGGAGCAAGTAGAATCATTTGTAAATAAGAACTTCACTTGGACTTAAAACGTTTGTGAATCCAAGTGTTTAGTTTCCAATGTTGATGAATCCTTTGACAGCTTTCTAATTAT Homo sapiens hg19 +snp_rs10737814 snp_rs10737814 1 chr1 237469150 237469346 - TCTGTAGGCTATGTTCAGAGTTTGCAGACTGAGTCCAAACCAACATCTTCTAGGCCCTCATAGTTTTATTGAAATACCTTTGTATCATATATTCCAAAATATGTATGTAAAGAAATGCATATTTTAAATAAAATTAACACC Homo sapiens hg19 +snp_rs10503087 snp_rs10503087 1 chr18 61476290 61476515 - TTTATTTCCCTGCTATGCCTGTGGAAATTGTGACCACTCCTTCTAGCCTAAGACTAAGACTCTTAGTCACACTGAAGAGTATTGTCTGAAGAGGCACAACCATGGGGTGGGAGAATGGTATAATGTAAAATAGATTGTTTTTAAAATATCTAGAAAGAATTTCTGCTCCATCC Homo sapiens hg19 +snp_rs10094564 snp_rs10094564 1 chr8 673385 673622 - GAATTTGGTATTTTCTCTAAACTGATGAAATAATGTGGTTTGTGTGTGTTTTGTGGTTTTAGTGGAAATGTTTTGAGAGATTTCTCTAATATGACAGGTGAAGGAGGCAGGGAGCAAGCACCTCCAAGCTGGCCATGGTGGAAATTTCTACTAATGATTATTTCTTGTTTGAAAATCTAATCA Homo sapiens hg19 +snp_rs11662907 snp_rs11662907 1 chr18 21455409 21455598 - TGGAGTCACTTTATTGCCACTCACTAGGCCATGGGCAACAGAGAAGCCAGGGGAGGGGAGCGTGCATGAGGTTCCCATACAGGACTGTTCACGAACATCTGGTCCACCCGAACACACAGAGGCTCAGCCTGAGGGAC Homo sapiens hg19 +snp_rs10093381 snp_rs10093381 1 chr8 87628221 87628447 - TCATATTTAGATTGGTTCAAATGTTTTTCTCTGAGAAAATCCAAGCCGTCAGCTGAAAGCTATCGATGTAAGTGCTTGTGTGTATTCCTGCCAAGAAAAGTGCTAATTGTTTGCTTATCTATGTTCAGGCTTGTCTCCTAGGTTGGTCTCACGTTTCCCATTGATCCGAC Homo sapiens hg19 +snp_rs10741808 snp_rs10741808 1 chr11 20020732 20020928 - ATAATAGACTGGGTTAAACCAGTCAGTCTCCCACAAGAGAAGTTCCTGAACATGAATAACCCGATTTTTTTGAAGGCAAGTTGGGCCATGGTTATCTCTCTTTGAGGACTGGCTGAGGACTGAGTGGGTGGGTTCACTGTGTGCCAC Homo sapiens hg19 +snp_rs11563212 snp_rs11563212 1 chr2 234869205 234869433 - AACAGAGACAGTACTAACAATACTATAAAAATATGGTAAGGAAAGCACTAGGCATTTTTCTTCCTCAGTAGCACTGTATTTCCAGCCACAGAGTAATAATATCTTCAACTTCTCTTTCAATCCTGTCTTGAGAATGAAGTTTATCTTTTTTCCGTTTTAACACAACAGAGGATTA Homo sapiens hg19 +snp_rs10514496 snp_rs10514496 1 chr16 80456253 80456446 - AGAGTGGCCGGAATAGCAGTAACCATCATGAGCTGGGAGACTGGACAGATGCCACATGACTCTGTGCACAGAAATGTTCTGAGAAACAGCCTGATCCAGAAAAGAGTGGTTTGAGACTGGCTTTTCAGAGACATTGGCAGT Homo sapiens hg19 +snp_rs11633318 snp_rs11633318 1 chr15 77602545 77602763 - AGCAGTTTACTTTGTTCAGAAAAGTTCTAAGTAATTTAAGTTCTGCTTAAACAGTGCTATGACCAAGCTAGGAACATAAGAGACTTGTAAAAGGAGTGACTCAGGGACCCCAGACTTAAACCTATTAGTTCAAACTTTTGTATGACTTCATGAACTCCTGAAAAA Homo sapiens hg19 +snp_rs10509550 snp_rs10509550 1 chr10 90219136 90219343 - TGATTAGCAAGCTCCCTGGATACATGGACTGTTTTAGTAGCGGAGGTACACTCAACCTTTCTGCAATGGTACAATACGAAACAGACAAAAAGAGCAAACTGCTTTGTATAGGCTTAGCATTAATGAATTTACTCTCTTTCTCAGCCCCAGTATTT Homo sapiens hg19 +snp_rs10758 snp_rs10758 1 chr2 113409836 113410058 - ACATCCTGAATAAAGATTGCAATACCCACATTCTAAGGTACCCAAAAGCCCTAATATAAACTTCAGCACACACCTGAGGATAGGCTATACTCTACGTTTGTAAGAGATGTCAAGAAATAGACTATGTTAGGATGTTGCTTACCTGACTTCATATCTTCAAAGACTAAAA Homo sapiens hg19 +snp_rs10281519 snp_rs10281519 1 chr7 90909877 90910063 - TTACCTGGATTAACTGATGCGAACAACAATGGTGCTTTGAAGCTCTTGGGTACAACAGTGGAAATGATCACATTTCTTGATTAATGAATGAATTCTTTCATAAGGATTTGTTTATGGAAATAAATAGAGTAATACCT Homo sapiens hg19 +snp_rs10860784 snp_rs10860784 1 chr12 102172883 102173072 - TTCCTGATTTTATAAAGAAATGTTCTTTGAGTTCTGCCACTGGGTTTAGCTTACCTGATTCTTACTTCCTCCTGTTGTATGTCATTTAACAATTTTGAGGGTGAAAGGATGAAGATGGAGTAGTGGTGGGGGAGCT Homo sapiens hg19 +snp_rs11077405 snp_rs11077405 1 chr17 76969721 76969928 - AAACTACTATATTTGTGGCGAAGAAAAACCTATGGGATTTCATTTTGAGTTAGGCTTTGAGAGGGGCTCAAAGAAGGGGAGAGGGTGCACCACACTGACCCCCGAGCCGGGAGCCTCCCATGACTTCTGCAGGCCTTCTCCCCGACAGGAAGCTGC Homo sapiens hg19 +snp_rs10449246 snp_rs10449246 1 chr1 224936145 224936337 - ATTTTAAGCATATTCTTAAAGCAGAAGAAAAGTCAACTCCTTCTGTGACTATAAAAGTAACAACCCCTCATATCGGTATTGCATTTTCTATACTGCAAATTGATTTCATGTAAATAAGCTTATTTAGTATTCACATCAT Homo sapiens hg19 +snp_rs10185855 snp_rs10185855 1 chr2 101642110 101642302 - TACTCCTGGAGCCATTGGGGCCTGAAACGGCGCCTTGTGTATTCCACAAACGCGTTCCTACTGCTAAGCAGTGAAATTCACCCAGTGTTGGTGGGTTATTGTGCTCTAGAGAGCATTTGGTCTCTTCAGTGTTATTTTG Homo sapiens hg19 +snp_rs10184153 snp_rs10184153 1 chr2 182220015 182220229 - TGAATCTCCATGAGAAGAACACTATAATGGCCACATCATAAAACAATGAATAGCTAAAATATATCAGGATTGCTTCTTAGGAATAAGTGCCTAAGAGCTTTGTGTACTTAATTTCAATTGTAATAATACTAATTGATAATTACTATTCTGCCCATTTTA Homo sapiens hg19 +snp_rs10771328 snp_rs10771328 1 chr12 27425214 27425411 - TGAGGGGAAATCAAAAGGAAAACAAAGCATAATATTTAAATCGCATGGCAAAGTTCTTAAACTTTTGCACTAATATACACACCCTAGCTAATTCATCAGCATAATACCATACAGCAGATCACCTCAGTACTATCTTTCCTATACAT Homo sapiens hg19 +snp_rs11563675 snp_rs11563675 1 chr7 126873773 126873967 - GCAAGGTGTAGGGGTCTAGGCATAGCATTGTGCACAGCCACTGTTATCTGTTTCTAGAATGAGGTCAGTCTCTGCTGTATTACTTCATTAGGCTCAGCAAGCTAATAGACATGTGTTCTCAATGTTGGCCATTAGTCTCCC Homo sapiens hg19 +snp_rs10148795 snp_rs10148795 1 chr14 33845151 33845373 - TTACAATCAACCTCTGTTTGATCCTGTGTGTCTGTTTTGAGAATGGAGATTTTGGTAAAACATGCATTCTTGAGATAATTTGAAGACCAGTGAGATAATTCTTGGCAAACCACAATAAGATTCTCCAGTGAAACCAATTCCGTAAGTATGAAACATTAATCTCAACAGAA Homo sapiens hg19 +snp_rs10516506 snp_rs10516506 1 chr4 104595082 104595313 - TTTTCAAGGCTAAAATGTTTCACTTCCTTTACCTATTAACTACTCTGCAATAAGTCTATTGCTCCTACCTGGGAGTTTCTTTCACTTTTATTCTTTCTAACTCCTCCACGTTTAAGCCACCGTTTGCCACTCCCTTTTCATCTAAAACCTCATTCTCTTATAAAAAATGAAATAAAAT Homo sapiens hg19 +snp_rs10178199 snp_rs10178199 1 chr2 127756794 127757018 - CCAGGCCTACCCACCACACCCCATCACTTCCCTCTGGCGTCCCTCTTGTTCGCTCTGTGTAAAACTCAATTTGCCTCTTGATGGATATGAATAATTAGAACCCTCCAGCATGAATAATTCTAGGCAAATTAATTTTCATGCCAATCAGGGAAAATTAATTGGCTTCATGATG Homo sapiens hg19 +snp_rs10516603 snp_rs10516603 1 chr4 115467309 115467500 - CAAATAAGATTCTATGGTGAAGGTGCGTGCATCAGAAAGACAATTTAAATGTGAGGTGGGGGACAATGGTATATGTAAACACTAGCGGGGCCAGATGAATTTAGTATTTTCGGATAACAGTGTCCGCTATGTATGTCT Homo sapiens hg19 +snp_rs10088698 snp_rs10088698 1 chr8 48654620 48654821 - TTTGGCAGGTGGGACACCCAACCCACAGAATCCAATTCTTGTTGTCAGTTCTGGCTACTTTACAATCTGGGGACTCAGCCTTTTAGATTCCAGAAGCTGAAGTGCACATAGAAATTGTTACCAATCACAGCAGGTTTCAATGACATGCAC Homo sapiens hg19 +snp_rs10103826 snp_rs10103826 1 chr8 135495908 135496102 - AGCTGCCTTTTAGCACGAAGAGAGCCCAGCAAAGTGCCGGTCCTGACAGTGATCTTGTCCAGACTCCAGAACACTGGAGACAGCGGAACAGCAGAACACGGTGCCTGATTCAGTGAATGATTTCTGCGTCCCAGGGGTTAAG Homo sapiens hg19 +snp_rs1042606 snp_rs1042606 1 chr10 112270522 112270712 - CCCTGTAGGGTTACTTTCCCAACTAGACGGTGATCAGCTTATGCCCCGAAGCAACAGAGACAGACATTGAAACTGCCAAAGTTCAAAAAATAAGGTGGAAATTGTGCTTCCTTCAAAATGAATTGGCTTCATAACTGC Homo sapiens hg19 +snp_rs10497276 snp_rs10497276 1 chr2 166856843 166857041 - ATGCCCCAGGACAAGTAACAAATTACTGTAAGTTGTTAGCCTGAGTATCCTTCATCCTGTGAGTGCCAAGTGTCTGCTGTACTATTGTTCACATTTCTTATTCATATTAACTTATTATCTTCAAGAATTTCAGAAAGAAAATA Homo sapiens hg19 +snp_rs10753764 snp_rs10753764 1 chr1 167760563 167760807 - ATGGGATTAAGATTAGTACAATTACTGTTAACTCACAGAAATAATAGAGAAAGAAATGCAAAGTGCCTGGCTCACACCAAGTATTTGGTAACTACTAGTTACTTCCATTCATGTCACCTGTCACCTCCACCCTGTGGCAAGCTCCTTGAGGAGCTTTGTCTTGTTTTGTTTCCTTATGCTTAGCACAGTGC Homo sapiens hg19 +snp_rs1002745 snp_rs1002745 1 chr10 82656133 82656340 - TTTTCTCAGTGGAGATGGTGTTTTATGACAGGGAACGGGTGAATTCCTCTCCTGCTCCACATTATAAAATCCTGGTCAAAATATCTATAATAAAATGCAAGACGAAAGGTGAGCAGTGAGGCTGACAGCTGGAAAGGGCCAAGAGTATATGCTTT Homo sapiens hg19 +snp_rs10073948 snp_rs10073948 1 chr5 82134466 82134661 - TCTGTCTTCTCAGCGTCCTTCTGATGTCCAGCTTTGTGTTTCCTGCTATGGACATTTCCTGAGATCACTTGAGCTTATGTTCCATCTCCGAGAGAAAGCTGATGAGAATTAGTCATCCATGAATGTGATTATGGGTGATAA Homo sapiens hg19 +snp_rs10830004 snp_rs10830004 1 chr10 133212057 133212291 - AAAGTAATCTCATGATTACTAGTTACCCTCTGATAGGTAATCGCTTTTTTAAATGGTTACAGTGCAGGCACTCAGAACTACTTTTTATAGCTGGGTGCCATGTATTTTTCTGGAAAGATGAACCGAGGAAATGATTTTCCAACTGTCATTGATATCTAAGGAAGACAGTGTGTCCACTGGGG Homo sapiens hg19 +snp_rs10128762 snp_rs10128762 1 chr12 74681738 74681939 - ACAAATAGCTTGTTTTTTAAAAGGACCTTTGTGAATGCATTTCTTATTAAGCCAAATGACATTATAAAATTACTTGCTAATGGATGCAGAGTTGCTGAAATGGTGAATGTTTGTCCCTATTAATAAAAACTGGAAGTAGAACGAAAAA Homo sapiens hg19 +snp_rs10109209 snp_rs10109209 1 chr8 5528789 5528981 - TACTAATGCCTCACCAGACTTTTGCAGTTCCTAACAAGTGGTCTTTCTGTTCTTGTTTTCACATAAATCTTCATGGTAGAACTTCAAACTTATTGCTCCCCGCTGTAAAATTACCCCTGCTTCTCACGCCCCAGCCCACG Homo sapiens hg19 +snp_rs1026580 snp_rs1026580 1 chr10 13980998 13981214 - TAGAATAATGTGAACCATACGGTTGGTACTGGCGTTGAATTCCCTGCAGCTGTTTCAATGGTCTTGCCTTACCGTGTAGCTGCCACTTCCTCTTAACCCTCGGGTTTCTCAATCTTGGTACTATTGACTTTTCAGACCAGATCATTCTCTGCTGGAGGGTGGG Homo sapiens hg19 +snp_rs10505299 snp_rs10505299 1 chr8 118426572 118426777 - TCTGGAATATAGAGTAGGGACCTAATGGGAGAGAAGACAGGAGAATTTGGAATGTCTTATGGGAGACATTGTTTTTGGATGGGGATCATGTAATATATTAACAAATAAGAAACAGCTAAAGGTTTTCTAGAAGATGACATGATCAAAAGTGTT Homo sapiens hg19 +snp_rs10919336 snp_rs10919336 1 chr1 170216650 170216862 - TTGCTTTTTTCTATTCCTCTTCTTCACTTCAGAGTTGGCCTAATCATGGCACAAATAAAGGAGTACTCTGTTCCACATCTTTTATGAAACTTTTGTTCCATTTACAAAATGGAGGTTATTAGTCCTGACTCTTGATTCTTAAGGCAGATAAGAATT Homo sapiens hg19 +snp_rs10505532 snp_rs10505532 1 chr8 130021793 130022003 - TAGTCGTTACTGATATGATACCCAGAGGGAAGATTCCTAAACAACCACCAATGAAGTCATTCAAAGTTAACTGAGTTATTCCCTTACCAAGAGTGTTTTGTATTGTTGCATTATGTAGCACCACAAACTTAGTGGCTTAAAACAATGCAAATTTATT Homo sapiens hg19 +snp_rs10518287 snp_rs10518287 1 chr19 35399234 35399459 - AAACACACATTTGCACCTGCAACAGATGTGCTACACCCAGTTGAACCCCAGGCACTCTGACTGAGGTCATAAGCTTTGTATTGAAGTCATCTGTCTCCAACCAGAGGTATGGCACTATCCTCTCTGATAGCAAATCAAGAGCACAGTGCTGGCATCTGGTGAAGACCTTCTTGC Homo sapiens hg19 +snp_rs10955157 snp_rs10955157 1 chr8 99226982 99227217 - AATTGGTGAAATGGACAGAAATTAGGACACCCAATGTTTTGATGGCTGTTTTAGGGAAGGCAAAGAGATACGAGTTTAATAGCTTTTGTAGCACTACTCAATTAAATCAAAGGTCTGGCAAATAAGTCCCATAAGAAACAGTTAAAATAATTGGTTTAATTTACCCGGAGAAGAAAAGACAA Homo sapiens hg19 +snp_rs10487324 snp_rs10487324 1 chr7 110036449 110036638 - ATCTTAAGTGGCGACTCTCAGGTTCATTTCACAATGAACTACATTTAGCATCCAGTCCAATGACATTTCTGAACTTTTTTCATATTGATCTTCAATTTTGGATCATACAGCAACAGTATAACTGGGTTTATTCCAGA Homo sapiens hg19 +snp_rs10519096 snp_rs10519096 1 chr15 61289759 61289993 - TGTGGGTTTCTGGTGACAAAATCACTTTTTAGAATCTTCTATTGTAGAGATGGGTAGATGGGACAGCAGCAACATAAATTTGAATTTTTTTTAAGCCATAACTATCATGTGGAAGATATACATGGGTGCTTTCTAAGAAGATAAATGTGAGTATTTGAGTATATCAGTAGACTATCTTAATTT Homo sapiens hg19 +snp_rs10968281 snp_rs10968281 1 chr9 28013135 28013339 - TAAGTCAGGCTTGGAGCAGGAGGAAAAGGTGAATAAGAGTGAAGAATTTAAAATACATATATAAAGGAGAAGAAAAAGAAATACAAAGACCAAAAGTGGAAGGCAGAAATAGGGAATTCTATGTGCCAAAATGTCTTTTATCATCCCTAAA Homo sapiens hg19 +snp_rs11060670 snp_rs11060670 1 chr12 130515566 130515760 - CCAGGGAGCCGTCCTGAGCAACAGCTGAAATCTCCTTCTGCAGCCTTCACATAGGAGAAAGCCGTCCTTGTGATGCTTCTGTTCGCCGTGGAAGGGATCTGAGTCTGCAGCAACCTCAAGTCTTGCCTCCCCAGAAAAAAGA Homo sapiens hg19 +snp_rs10859402 snp_rs10859402 1 chr12 93409694 93409895 - AGCAAAACAATAGCATCACTGCCATTCGTGCCTCAGCTTCATGGTGGGGCGGTAGGAGAATGTGTGTTTTGCCTGCTTTGTTGCAAGGAGGAAAGGGAGGGTTGCTCTGTCCTGGTTGAGGAGGCAAAGGTGGCATTCCTGTATTTTTGT Homo sapiens hg19 +snp_rs1108958 snp_rs1108958 1 chr13 51822032 51822226 - TATTCTCATTTGTATGCAGTTATCTGATAAGCGTGTGCCCCCATATAGACCTGAATCATGAAAATTCATCATGATGGCTAGGAACACAATCAGAATTCAGAGATAATTCTGGCCCTTTTCTTTGCTTGCCCTTTCTGCCTGC Homo sapiens hg19 +snp_rs10869756 snp_rs10869756 1 chr9 78959172 78959384 - TCATGTGCTGGAGTCAATTGTGAATGGGCACAGACTGGGAACCATGATATGGTAGAGTTTTTATGGAGTTGCTTTAGGGGCTTCCTGGGAATGGTGGGTGGTGAGGGGAGCATGGAGAGGCATCAGATGGGGTTCTGGGGTGGCTCCTCTGCTCCCACC Homo sapiens hg19 +snp_rs10502370 snp_rs10502370 1 chr18 8454350 8454541 - CATTGGAACCACCATCTTTGAAGAGTGTTTAAGTTCTGTGTAGAGGTGTTGGGGTCTTTTATGAAAAGCAGAGGCCTGGCCAGGAAGTCAGGACGACCACTACCCATGTCCTGAGAAGGTGACCCAAATTCACTCACA Homo sapiens hg19 +snp_rs10000030 snp_rs10000030 1 chr4 103374004 103374198 - ATCTTTTCTTAAGCCCGCTGTAGTTAAACCTGCATCATATTGAGCCAGATAGAATCTCATGAAACAGTCATATCAAACAATGAAACATATGGCTATATGCAATTCATAGTTTATTCTTATTTTTAGCAATATAGACTTT Homo sapiens hg19 +snp_rs10746432 snp_rs10746432 1 chr1 210837539 210837734 - ATCTGATAGGGGGAAATGATAAGGTGGCTTGGCAGCTGTATTTAAATCTTATTTACTCTAGTAGTTGCAGTCTGGAGATATCATGGAGTCATTCATCAAATGGCCCTAAGCCTGCAGACCTTCCTCCAGAGCTAAATTTA Homo sapiens hg19 +snp_rs10438441 snp_rs10438441 1 chr15 92862458 92862657 - AATCACAAACCCTGCCCTTCCAAATTTGCTAGCCACTTAGCCCTTGTTGGAATTACCGTACACATGGGGCAACAGTCACGCTGTGGTTCAGGGAGCCCTCCGAGCCCAGGGCTTTCCTTTCCCTTGGTGCCACAGTGGAGATGCTG Homo sapiens hg19 +snp_rs1110240 snp_rs1110240 1 chr1 21324778 21324997 - TTACATTTCTTTGTGCTTTATTCTTAGGTAACAATAGGTACATATACACAGTGCTTTGCTGTTGTCTATAGTAATTAAGAGATTTGACTTATTTACTCTTTTTTCTTATCAAGCCTATAAGAATACCACTTGGATTAATCATGTTAGAGACTGATGTTCTTTACTA Homo sapiens hg19 +snp_rs10110604 snp_rs10110604 1 chr8 16502925 16503123 - AAAGTAGAGACTGTTTTGGCTATGAAAATAGTCCTGGTCACAGCTCCCACCAAAAAATGAAAACTTAAAAATAATGATAATTTTAAAAGCTGGGATGTATTTTTTAGGGCCGAGGAAAGTTTCGCACTGAGTTACTTGAGATAATG Homo sapiens hg19 +snp_rs10502432 snp_rs10502432 1 chr18 19827323 19827515 - AGACAGAAATTGAGTTGGAGATCCCAAGGCCTTGACACTGCCTTCCTGTCAAGGGGTAAGAACTGTGGCGATGAGAGGGAGGGGAGAGAGAGGGGGCAGTGTGTGCCACCAGCTTCACCTGCCATGGTTGCCTCCAGCC Homo sapiens hg19 +snp_rs10874743 snp_rs10874743 1 chr1 91951952 91952160 - CAAGAATACTATCGAATCACTTCTGCACAAACTTAGTTGAGGTCTACAGGAAACAAGCAGCAGCAGCAGTGGCTGAAGTGAGAGGTCTGGCTGGTAGGATTGAAGTGGTGCACTGTCCAGAGCTGGGAAGGGTTTGAATTTTACCCTACTTGCAA Homo sapiens hg19 +snp_rs10090419 snp_rs10090419 1 chr8 124028479 124028669 - GGTATCAGATCATGCTCTCTGCCTTCAAGCAAAATTTTAAACATTAGGATCTGCTAAGTGGAATAGGTTTAAACACATTCTCAGTTTACTAATAAAAGAGTCAAAGATGGGAAATAGTTGGAAAATACTATTGAGAGT Homo sapiens hg19 +snp_rs10496687 snp_rs10496687 1 chr2 133269105 133269307 - TTGCTGTTATTTACCAAGACAGCAAATGGTCCTGCACCCTCACCTGGCTACTTTAGAAAAAATCACCTTCCGCAGCAAATATGACACTTCTCTGATTAGCCACACCACAAGCTTGTCCAAAGAGTCAGAGTTCTCCCTCAGCACTACAT Homo sapiens hg19 +snp_rs10790037 snp_rs10790037 1 chr11 114665009 114665207 - CCCAGTATACTGAGCACTCAGGACATGCCACAAGATGATCTGGAAGTGAAGGGGCACCTAATTCATCATGATTGGGCCAACTAAATGTCCCCAGAGGCCACACTAAGCTGAATCTTGAAAAATATTATTGCAATATGAACAAGCAGG Homo sapiens hg19 +snp_rs10895457 snp_rs10895457 1 chr11 103416499 103416695 - TGAGGGTTACCAAGTGTAGGGAAAGAAATTCATGATGGATTTCACCATTGCTCCCAGGATAGCTCCAGCCTGGAACCCAGCAGACTCACCATCAGGACAAGGAATGTGGCTTTCTGATTTAAAGATGAGAGCAACTAAATTTA Homo sapiens hg19 +snp_rs12604608 snp_rs12604608 1 chr18 42405927 42406123 - TATTGGCCTCTGTTGACCTTCCTTGAGAGACGACATGACATTTTCAATCACATTTAGTTACAAAAAGATTCATCTAATATTTATTGAGAACCTACTAAATTCCAGGTATTATGCAAGTCGTTTGCTTATGCATTTAACTCTT Homo sapiens hg19 +snp_rs11171681 snp_rs11171681 1 chr12 56193075 56193282 - CTTTCTGATTTACAGTGGAGGATGGGAGGACAAAGTGCTAGAATGGAAAGTAGATCTTGATTTGTTTAAACTGTTCCACAAGGGTGATCCTAAACATCTTTAATTTGGGGCTTTTTCCACAAATGTCTGGCCATTTTGTACTATAGTACATTAA Homo sapiens hg19 +snp_rs10961505 snp_rs10961505 1 chr9 14410433 14410646 - TTCTCTGAATCACTCTCAACTTTCTTCCACCACAATCTAAGGCAAGGCTGATTTTAAAGTACTTTTTCATTTCCCTTTTATTTTTAGGAGGTTACCAGAGGCAAAGGTAATCATGCTCTGATGAACTGTAACTCTTCCCAAATCTCCTAACCTCTTCTA Homo sapiens hg19 +snp_rs10497933 snp_rs10497933 1 chr2 212141525 212141718 - TCTTTCATGCCCATCTTTTCTCTTCCCTCCCAGAATTATTCTTTGTCTTCTCTGTGGTTCAATGACATGTACCTCTATTATATCAGGTTTCATATTCTTCACTAGATTACAGCTATTTATACATGTGTCCTTCCTTTTCAC Homo sapiens hg19 +snp_rs12587583 snp_rs12587583 1 chr14 69510292 69510482 - GAGTCACAGCTTAGTTGTCTTAGAAGAGCAGAAGTAGGAAGTCAGAGAAAGACGAGGGCCTCGGTGGGGTGGAAAGTGGGGGTCCCAGAGAGCATGAGGTAGTAGGAAGAATGTGATGTTTAATCACAGTGTGATGCTTTG Homo sapiens hg19 +snp_rs10966009 snp_rs10966009 1 chr9 23651277 23651483 - CACAGGGCCCACAATCATCGGACACCTTGCGGCTTTTGCGTGAGCTTATTCCTGTGTTTGGAAACGCCCCTGCCTTGTCTGTACTTCAAGAATCAACTTAAGCTAGCTTCATTCTCCCATTTCCACAAAAACTTCCAGAACTCTGTACACATTTC Homo sapiens hg19 +snp_rs1160246 snp_rs1160246 1 chr9 119992935 119993131 - GTGGAATCTTTCGTCATTGCTGATGATGCTACCTTTCCATGATGCATGCACTGTCCGCTCCCTCTGCCCCAGAATAGCCACTGAGGAATGAGAAAAGAGGTCTTATTTTCATTCTCTCTTAGACCTTTTCTTTCCTGGCTCAAT Homo sapiens hg19 +snp_rs11096672 snp_rs11096672 1 chr2 20743564 20743772 - CGGGACCAGCTGTCTCCACCAGCTTCTTTCGGAGGCTGGGTAAAATGTGTAAGATGCTGGACCAGGGAAGCCACTTGATTGCCTTATGTCCAGGGCACCTTCCAGACCATAGAGGCCTGCCACAAATCCCTGGGAAATTCGCCTTTATTCTGCAGC Homo sapiens hg19 +snp_rs10926264 snp_rs10926264 1 chr1 235778986 235779175 - CCCATCCATCATGGACTGCTTGCCATCCAGTTCACTGTGGCAGTGCTGAGGGCTCATGTGGTCCAGGTCCCCATTCTGCAGCTTCTCCATCACCCCCCTCCTCCTGGTGCTTCTTGGAAGGAAGCCTCTCAGAGGCA Homo sapiens hg19 +snp_rs10050018 snp_rs10050018 1 chr4 183349468 183349656 - ATCTTTGGGAAAGTGAACGTGGAGATAAAATGGGAACATCAGTCAGCAGTGGTGGCGTAAGCAGGAGAAGCAAAGCACATGGGAACTAGACAGGTGGCTACAGTGAGGTACCTATGGCATCTCTTTATGCTCTCT Homo sapiens hg19 +snp_rs10243669 snp_rs10243669 1 chr7 45915758 45915965 - TATCAGTCCTTGTGATAGAAAATAATTACACTATAGGAGGTCAGGGTTCCTCACCAGGTAAGAGGGTTGTCATGGTAGTCATTTGAGTTACTGTTTTCTTCCTTGTGCTCAAGAGGGCCCTCTGGGAAAGTCATTGTGGTTTCTTCGTCCTCTACA Homo sapiens hg19 +snp_rs10767843 snp_rs10767843 1 chr11 30436224 30436446 - GGACCACAGGAGCAACCTAGCTTTCCAAAGCTTTGGTCATCCGGAACCACAAGGGGTAAGACTTAGTGTATCTAAAGAGAGCTGGGTATCTTGTGACCAGTTTACAGGCAGCTCCTCTCAGTCCTTCTTTGAATCATCTTAGAAGTAAACTGCTATAAGAAAGATATAAT Homo sapiens hg19 +snp_rs1040173 snp_rs1040173 1 chr2 146120361 146120549 - TCCTCTACTATAGCACGTATTGTTCAGAGGATCTCATATGGCATCAATTAGAGGGCAGACCTTGGGCTGAGGCATTTGTTTTCTGCTGACACCTTTTGAAATCCCCATTCCTCATTCACTGGTGCTCTAGTTTTTA Homo sapiens hg19 +snp_rs10490012 snp_rs10490012 1 chr2 234843344 234843570 - AAGATGGTAATAGTGATATGCATTTCTATGACTTTTCTAAAAACACAATAGGAGCAGAAATGAGTTGCTTTATGGGCAAATTTTATGACCAGTCCAGAAGCAGATGGATTCCCAGCCAAACTGTGGCCAAGTTTCTGCTGCCTGAAAGCAATTGGCTTCAACTGGAGTTGCTCT Homo sapiens hg19 +snp_rs10500844 snp_rs10500844 1 chr11 19250005 19250225 - ACTTCTCTCTGTCTTATTTTTCCGCATCGGTAAAGAATTTATTCCACCAGTTTTTCCTCATCACCTACTGGATATAAAGCACTGTGCTCTGGATCAAATCTAACCCAGCACCTGCCTTTGGTGGCAATTGCTTTTGGGTACTTGCCTGTGGGCATATGATAGTTTTT Homo sapiens hg19 +snp_rs10143478 snp_rs10143478 1 chr14 33442462 33442696 - AAAGTACATTTTTAGATGAAACTTGGAACACTGTTTTCAAACAAATGACTTTTTAGATTGTAGTTAGGTGTCTGATCAGCCCCAGATGCCTGTTTAACCTTAACATGGCAGAATAATGGACCATGTATTCCCAGAATAAAGACTAAGTCAGTGAAAAGGAAATTTTAAAAAAATTAATA Homo sapiens hg19 +snp_rs10493230 snp_rs10493230 1 chr1 58049953 58050179 - TCAGCTATGGAAGGAGCACACTATTCCAAGGACCCAGAGAGATCTGCTGCATCTTAGCAGACACTGTACAGAGCTTAAGGCCTCAACCAGCCCTGTGATTTGATAAAAGAAAAACATCAGCCAAATTAAATTTAAAGGAGTTTAATTGAGCAATGAACAATTTGTGAATTGGGC Homo sapiens hg19 +snp_rs10489562 snp_rs10489562 1 chr1 96058387 96058598 - CCAGGCTGTCTACTGGCTGGAGCTAAGCTAAACACTTGTCACCCTTCTATAAGTGCAGGAAAGATGGCTTGGGAAACCTAAAGAGAGAGAAAAGTGTTTCAACAGAGTTATGATCACACAGTGAATGAAGTTTCTAGAAATGGTATAATGCAGTGAAAA Homo sapiens hg19 +snp_rs109894 snp_rs109894 1 chr5 79067918 79068134 - ATAAATTTTTGCTTAGCCGGCCCCTAATATGCTTGCCTGCAACAAGAAAAATAAAAATGAATTGATTGGCAAGATCTCAAATAGAATAAGCTAATGACAAGCCTTATGTTTTAATAAGCTCGATGTTGGTCTTAATGAAATTGGTGGATGGTCTTTTTTTTTT Homo sapiens hg19 +snp_rs10914880 snp_rs10914880 1 chr1 34620621 34620809 - CATTAGCACTTTATGATCACCTCTCTGTGCAAAACTTCTCTCTTATTTACAAAGTTTGCCTCCCTTCATCCCCAATCCTGAAGCTAAGCTATCCCAATCCCAATAAGTACTCATTCTGATGTGTTTGATATATGTC Homo sapiens hg19 +snp_rs11662069 snp_rs11662069 1 chr18 29829195 29829384 - GTTCCCCATCTTTCCGTTGTATCTTTTCAACAAAGGTTCAAAGACCAAGTATAGCTTGAGCCAAAACTTCGGGGTGCTTTCATCTGTTTAAGAACTTGAAATCTTTATCCACTACTAACTCTGTCCCTCTTGATGCCAA Homo sapiens hg19 +snp_rs10996274 snp_rs10996274 1 chr10 66956996 66957203 - TCTGTCTGGAGAGTACATGTTTTTACTCCCGTCTAACAATGAACACCTTTCAAAACATACTGAGTTTACTCCATTTCATGTTTGTCATCCCTCTATTCTTTCAGACCTGTATTAATGAGCTCAGGTTGCCATGATAAAATACTGTAGACTGGGT Homo sapiens hg19 +snp_rs10849968 snp_rs10849968 1 chr12 109694168 109694359 - GAAGTTTTCTGGGGAGAGCACCCAAGGCCACCTTCTGATGCCCAAAGGGGTTGTTAGCCCTTGTGGCCTGGGGACTGACTACAGGGTCCCAGGCCTCAGGAGGAGGCTGGCTGAGATACCTTCTAAGGGCACACACAGA Homo sapiens hg19 +snp_rs10496397 snp_rs10496397 1 chr2 106184288 106184481 - CCAGACGCTCCCTAATGGTTTTGCCTGAGTCTCTGGCATCAGAATTGGCAGGTTCTTGTCTACAGGTATTGAATGCACAGGGTCTCACTTCTTACTGAGAAACTACAGACACAGGGGGCAATGAGAAAGGAAGAAGCCCC Homo sapiens hg19 +snp_rs10744116 snp_rs10744116 1 chr12 16476721 16476917 - ACAATCTTTGTCTCTTAAGTTCTCCCAAGGCCACACCTAAAAAGGGGGTTATGTTACCAGTGTTTGGTGTCAGTATCACGGAAGCCCAGGCATTATTTTAGTCTGTAGTTGCCAACATGCTCATTGCTGGTTGAACAGGTCAGTA Homo sapiens hg19 +snp_rs10521575 snp_rs10521575 1 chrX 116625894 116626091 - TAGCCTTAGAAGCATCATGTATTTCGAAAGTGGTATTTTACCCTTCATTAAACCTTGTATTACAAAGAAAAAGCTGTCTTTGTGACATTTAAGTAGGAAGATGTTATGATAATATTTAATGTCTAGAGACAGACAGACAGGATT Homo sapiens hg19 +snp_rs11104117 snp_rs11104117 1 chr12 87224875 87225091 - AATGATTCGAGCTTCAGAAAATGATCTACCAGGGATTTTTCTTTCTTCTTTTCGATTATCATTGTGGGTTCAAGGTTGGGAATATTCAAGGAAAATGGATATCTTTATGAGAATAGGTAGAATTTACATGTAGAAATGAAGATTAACATGGCAAATTATTGAA Homo sapiens hg19 +snp_rs1060912 snp_rs1060912 1 chr6 52389558 52389764 - TCTATTTGCATAGCACCTTACAGTGTGTAGCTCTGTGAGAAAAGGTAGATGGTTTTATCCCATTGTTCAGAAGGGTTAACTGAGACAGAGGGACCCTGGGTCATATGACAGACAACTGATGGCTCCAGAAGTGAGCTCCAGGTCTTTTCATGC Homo sapiens hg19 +snp_rs10865643 snp_rs10865643 1 chr3 69099573 69099803 - AACTTTAGATAAGATAGAATATAGGTTTTACATATAAGGATATTTGTTTTCGGAAAATGCCCATAGTCTTCAGAATGGTATAATTTAGATGGATACCAAATAACCCTGGGATTATATAAAGTATTCTCCAAGAGGCAAAATTAATTCCTGTCATCTTTTGAATGTATTTAAATTAAT Homo sapiens hg19 +snp_rs10153199 snp_rs10153199 1 chr16 860524 860710 - CCTGCTCCAGAACCCAGAGGTTCCGGGCCAAGGGCGCACACGGAGTTTGGGTTTGTGCTACTTCCCTGGGACATCCTGATGTGGCCTGTTTGGGAGAAGCCGCCAGGAACACCCTATCCTGTTGGCTCCATGTCCC Homo sapiens hg19 +snp_rs1002897 snp_rs1002897 1 chr2 66464173 66464394 - TTGTGACCCGTACCACTGGCCTGTCTGTTAAACAGTGATTACAGTTTATCTTTTCAAAGTCAGTGGGCAGGACCTACTGCTCTCTGAAGTACCTCTCAATTCTAGAACCTGAAAGTCCAAGTAAAAAGAAATAAACATTGTACTAGAATAGCGCCTTTTTTTTTTTTT Homo sapiens hg19 +snp_rs11113551 snp_rs11113551 1 chr12 108248152 108248371 - ATATTTCCGAGCACAGTTACTGCTTCCAGAAAGATGTGCATATAGAGCCCTAAATGCTAAAAGCAATGTATGGCACACAAATAATTTATGATGTGCCCTTTTCTTTCACTAAATTCAACATGTATTAAGGAAGAGCAGTTTCTAAAGAAACAACTTGTTAAATCTCA Homo sapiens hg19 +snp_rs1030356 snp_rs1030356 1 chr4 141826627 141826819 - TCTCCACCCCTTTCACTAGAGGAGCAGGATTCAGCATGACATCGCTCTGTTCATTGACAATTTCTTTACCAATTACCCCATCTTCTTCCCCTTCTTTTCCATTTTTATTGCCTCAAGATGGGTGATGGGGTCAAGAATTA Homo sapiens hg19 +snp_rs11048057 snp_rs11048057 1 chr12 25623812 25624027 - CAAATCCCTTGGCTTATTTTCTACATCTGCTCTTTTTTTCTACATCTGCTAATGTCTCCTTTTCCCAAGGCATGAAGGTGGAAAATCCTACATGCTTGAGGTGAAGAAAGGGCCTTGGGGTACAAGTAAATTCAGAGGAGATACACACCAGTGCTGGTAAT Homo sapiens hg19 +snp_rs1156232 snp_rs1156232 1 chr4 126433063 126433260 - TTTCCAGTTTCCTCAGTTTCAGTTGTCTAAAATTGTTTCGAAACCACTGAGTTTTTATTTTCTTTTAAGCAGAGGTCAACAATCAGCCTTCAGATGGTTCAAATTAGTCAACATAGATCAGAGCTGAACCCATGCCCTAGAAGTGA Homo sapiens hg19 +snp_rs11074037 snp_rs11074037 1 chr15 92604308 92604497 - CCTAGACTCATGGAAGGAGAGGGGAAACCCAGAAGAACAAGGATCATTTATTAGGCACCTATGTATACCAGACCCCAGTGCAAAGGTAGAAAAGAGGGAAAATGCTAATTCACAAACATTAATTTACAAACACTTACTC Homo sapiens hg19 +snp_rs10257276 snp_rs10257276 1 chr7 136370660 136370850 - AGATTCTGGTCTGGTGTCCTTTCTGCTATTACACACCAACTTCAGTGCTGCAAGATATTACAGCAGATGTGTTGCGGTTCTGTCTGGCATAACTGGGAGTAGCTGAAACTCAAGCAATTTGGATGTGCCCGGGGAAT Homo sapiens hg19 +snp_rs12588458 snp_rs12588458 1 chr14 67830703 67830911 - TCCTTGAATTCACAATGTCTAGCTTCTCTTATCCCCAATACTCCCAAATATTCCTTTCTTTTATTGAATAGGTATACCTAATCTTGAGAATAGCTTTAATCTCCATTACTACAAAGTTCAAGTTTCTCTTAACCTCCAAGCATTAAAGATATTTA Homo sapiens hg19 +snp_rs10077711 snp_rs10077711 1 chr5 179587592 179587795 - GTGCATGGCTTCTTGCTGATGTGAGACCCTTACTGGAGAAATACTCTTCTGCTTGCTGTTTTCTCCACTGGGCACCTATCTAGAAGTTAATTTTGTATTTTTCAGCTTTAAAAGTTTTCCTAATACTGATGACATGCATATTGTGTGTGGC Homo sapiens hg19 +snp_rs10279558 snp_rs10279558 1 chr7 114862779 114862986 - CAGATCAGACACCCCAAATATTGAAATTAGCTTATTCTGGAGTTGAGTTTGCCCAACTTCACATATACTTATGACACTGGAAGGTCAAAAATTGATCTCTCCTATTCAAGTCCTATAAAAAATAATTGTCTACCACCTAAGTTAATTTCAAGTT Homo sapiens hg19 +snp_rs10508853 snp_rs10508853 1 chr10 37069230 37069440 - TCCACTGAAGCCCATTTCTATCAAGTATTCTCTCGGCCAGAAAGGGTAACACCCGATATATACGCCCCAATTCCTTCACCTTTGTGCACAAGCCAGCCTTACTATTCAAATATAGAACTACCCACTGAGCCAGAACATGACCTCAGATCCTTAGAGG Homo sapiens hg19 +snp_rs10793421 snp_rs10793421 1 chr7 54704855 54705047 - ACATGTATTGTTTACGAACAGAAAATGCATGGTGGGATACATGTGAAAATGGCAAGAATGGTTGCTTTTGGGAATGGGGACCAGGGCTGGGGACTCATGTGGGAGTGAGTTCTTACTTTCCACTGTACATATTCCATGTG Homo sapiens hg19 +snp_rs10432009 snp_rs10432009 1 chr17 13091291 13091497 - ACATTATTTTTGTAATTTATTTTACCCTTATCATAAAATGCTTTTCTACAGTATGCTTTTCATAGCCATGTAGACTTTACCATTTTTGGATCTTACAATGAGGATTTTAATTTTTACATAATCCACCTATCAGTCCTTTTACAACTCAATT Homo sapiens hg19 +snp_rs11002643 snp_rs11002643 1 chr10 80478352 80478539 - AGTTCATTGCTGTGCTCACCAGAAAGTGGTCAGCAGAATGTTGCTTCTGGAGAAGTTAAGTGCAGGCTAGCAACTCCTCAGGGGTTCAGTGGATGAAAGGCTGCAAAATAGGGTTTGGAATCGCTTCATAGACAGGG Homo sapiens hg19 +snp_rs10519010 snp_rs10519010 1 chr15 60551765 60551969 - CCCAGTGAGTCCCATAGTTCAGTGGAGGAGTTTAATATTCTTGAGTGATAACTTGATGAATCACTCTTCTTTAGTGTCTGTGGTAGGAGTCAGCACTGATTACCTAGACCTAGAGTAACAGTCTTGTGGACAATCAAATTACTGTAAATT Homo sapiens hg19 +snp_rs11576172 snp_rs11576172 1 chr1 217324503 217324702 - GATTTTGACACTATGTCAAGGCTGTCCACTTCCGAGGACTAGACTCATGTTACCAGAGCTCATGAAAGACTGATGTATAAAACTAGGAGAGTGCTTCAGAGTGTGGGTGAGGATAAAACAAACTAGAGTTTGAATCCTGGCTCTG Homo sapiens hg19 +snp_rs11133601 snp_rs11133601 1 chr5 10104416 10104649 - AGTAGGGAAGGGAAGGAATATTCAATAAATGGTGTAGGAACAAATGGTAAGGGAAATAGGAAAAGAAATAGGGAATAGGAAAAAAGGAAATAGGAAAAAATATTCTTGTAAACCGTCCTATATAACTAAATACTATGTAACTAAGTAAATTCCAGTTGTATTTAAAAGTTAAATATAAA Homo sapiens hg19 +snp_rs10215963 snp_rs10215963 1 chr7 26583629 26583841 - CCAGCACCAGGCAGGAGAAATGAGACAAACAAGCTTTGAAAATAAATCTGACTCTCTCGCGGCTCCGGATAGCCGACAAGTGTTCGTCCATCTGCCGCAAGCGTTCACACTGTGAATTCATTGATTTGATAATACTCTCGCATAATTGATTAAGGAGAGAC Homo sapiens hg19 +snp_rs11265625 snp_rs11265625 1 chr1 153642759 153642954 - AGGGCTCACTGAGCCCCATCATTACTTGATGGGGGTTGGATTAACTTAGAGGAGGTTATGGGGGTGTAACTGGGCACCATTTGGAATGGGGACAAGTGTAAGTGTGAGTGGGGTCTCTTGCCTACCGTTGGGAGGTTCCGAG Homo sapiens hg19 +snp_rs10489391 snp_rs10489391 1 chr1 210458696 210458902 - CAGTAGATACTTAATAGTCAAAGCTGCAGGAAGAGAGCCTTTGTCTCACTTGAGTCAGGCACATCTAATTGGGAGAATCTAATTCTCTTCTAGAAACCTAGCTGCAAGGTAGTCTGAGAAATGAAGAGTTTAGTTTACCAGCCTCTGTAAATC Homo sapiens hg19 +snp_rs11024021 snp_rs11024021 1 chr11 16735341 16735565 - TTTTTATTATGGCAATTAAAAAACATATTCACACATGGGCAGAATCGTGAGTATGGACACCATGTGCTTAGTGGGGAAGTAAAACATTTTTGGCAAAGAAAAGTTGGATCACAGTTTTCTCCATTGGTTCTCCAAGTGACAGGAGCAACTTGAGATGATTTAGTAGCTGC Homo sapiens hg19 +snp_rs1034826 snp_rs1034826 1 chr7 108083455 108083662 - TACAAAAAAAAAAGGTCTAATTGTTTTAAATAATAGCAACGAGATTGTTTGGTAGGAAGATTCTTGGGATGAACACTGAGAACTTTACAATTCTGAGTTTGTGTCATTCACTGATCTCATTTTAATACATGGACCATTTGCCAATTTGAGGTTTC Homo sapiens hg19 +snp_rs10901226 snp_rs10901226 1 chr9 133483063 133483259 - GTCCAGAGTCAACTCTGAGCTGGCAGATGCTTAGGAAGGATAAATCATCTCCCTCCTCCATGCAAATGCTGGAGTCCACCCAAGGCTGAAACATGTGATTGCAGTTTCATTCCCTTCGGAACATTCCCATTTGCTGCCTAAAA Homo sapiens hg19 +snp_rs10997716 snp_rs10997716 1 chr10 53235867 53236086 - AAAACTCAATTCTTCAGGACTCCTGCAAATATTGACTGGCTCACGTCCTTGCCTGTATCCTTCAATACTGTAGGCCTCCGATCTCTACAGGTCTCAATTCCAAGGAACTTCCCATTTCCTTCTCAATGACTGTGATATATGGATGTCTTTTCATCTTCTAACTATT Homo sapiens hg19 +snp_rs10739688 snp_rs10739688 1 chr9 129772346 129772550 - GAGAGAGATGAACAACTAGAGCCTGGCCAGGTGTCCAGGCTCTGGCTCCAGCCTCTCCCCACCTCTAGCCTCCATGACACCGCCCCGTGAGGATGGCCAAATTCCTTGTTTGGTCAAGTTGGCTTGCCAGACTCACCTGGCCTCCCACTGTTC Homo sapiens hg19 +snp_rs10903900 snp_rs10903900 1 chr10 2990103 2990301 - TGTTTTCTCTCTTTATTTAGGTGAAGCATTAACAAGTCAATAGGCTTAACTTAGATATTCAGAATATGAAACCAGTCACTTAAAAAAAAGCTTTATTTTATTCAATAAAAAGATTGACAGATAATTATTACATCTACCATGTGG Homo sapiens hg19 +snp_rs10192459 snp_rs10192459 1 chr2 152517828 152518027 - TGCCTTTGATAACAGAGAAAAAGATGATTTGGATCTAAACGTGAAACAGTTGCAGAAAATAATGGCCATAGTTGTGCTAGAAAGATAGAACTGTATTATGCTAAGCCACGGAGCAAACCCCCTGGAGTCTTCAGAGAATTGAATGA Homo sapiens hg19 +snp_rs10860066 snp_rs10860066 1 chr12 97073116 97073344 - CCAGCAAGTTTATAATTCAGAGAATTTCTTGGTCCCAACCTAAAGCCGCTAAATTCAAAGCCCCCAGATCTGCAGCAGGTGTTTCAACATTCAGATCAATTTTTTTTTTCTTTTAGTATACCAGAAGGTCCTTTTAAAAAAAAAAAAAGCTTGGAAAACTTTTGATTCTTATGAA Homo sapiens hg19 +snp_rs10184780 snp_rs10184780 1 chr2 20054242 20054430 - GCCGGGCATTCCCAGCTCTTTCTAGGGTGGCGAGCTAAGGGTGACTAGACTCCATAGAATTGTGCCCAACCTGAAGCCTATTCCATTTGTGCCCAGCTTTGCTGCCTTGGGGCCTTTGCACTTACTGCTCCCGCTGC Homo sapiens hg19 +snp_rs11152428 snp_rs11152428 1 chr18 61994541 61994754 - TTTAAATGAACAGATATTAGACAGCCTTATAGGTTTTCCAGAAATACAGGGGAGAAGTTTTCAAAGGGCTTGCAGATGCTGAAATTGCAATAGGAAGAGAACCATATGAACAGTCTTGTGGCTGTCTTACTGAAAGGTAAAGGTAGGATTTTTTTCCCC Homo sapiens hg19 +snp_rs10925402 snp_rs10925402 1 chr1 237559299 237559489 - TCCTTCAGGAACTGTCAAAATTATATAAATGGGGGACCTCACAACCAAGGGTGATTCTCTATACAGCCATCCTTAACCAAACTTACATTAAAGTGCAAGAGTTATTTTTTCTCCGTTTCTTTCTTTCACAAATACGAAA Homo sapiens hg19 +snp_rs10111409 snp_rs10111409 1 chr8 133118324 133118522 - TTCTCCAATCCAAGCGCACATTCTCTTGACTTTTCTTCCCGCCCAATTCACCTTCCAGATAAATCCAACCCTCTACCAATGGTAAATTTCTCCTCTTTTCAAATCGTATCTGTGCAGCCTGTATTTAAATTGTCATTACATTAATA Homo sapiens hg19 +snp_rs1011539 snp_rs1011539 1 chr7 14294433 14294637 - GTGCCTTGCCACGTTTAAAAGAAAAACCCAGTTGTTTACACTACCCAGTGCTAGGGACATTGTTAACTCTAGGGAATGAATCCGAATTTGTGAATACTCATGGTAAGAAAATTCCTTACAAGGTATTATGGAAGGGCTGAAGATGGGGTAA Homo sapiens hg19 +snp_rs11084990 snp_rs11084990 1 chr19 3009070 3009261 - GCTGGAGTTTTCAGAACCCTGGCCTAGAGCCAGTCTGGGCATTGGATGGAGAACCCTTCAGGATCCTTGGAACCGTGGAGTTCTAGGATTTCCTGGATAGAGATTTTGGTGTCGGTGTGCTCAAGTGAAAACCTCAGCCC Homo sapiens hg19 +snp_rs10122609 snp_rs10122609 1 chr9 9283394 9283595 - TGTCATTTTTCTATTTGTTCTATCACTAGTGATAATTGGGCTTACTTCCTAGCAGTTGGATACTTTCTGTAAAAAAGAAAATATAAAGCTAAAATTATAGACATTATGCTGTGCCTGAAAGAGAAAAGAAATGAGAAGATATAATTGAA Homo sapiens hg19 +snp_rs10208207 snp_rs10208207 1 chr2 169074793 169075011 - CGCTGTCCTATGACCTGACCCTGGTATGCATGGTGCTGTGCCCTACGGTCACTATTTTTGATGATAGGACTTTGTCCAGTCAGCTTAGCGGAAAAGATCATACATGTTGAACACTGCGAAAGTGAACTTTCCCAAGATATTCTTTTGGGGAATTTTCTGAGCTTT Homo sapiens hg19 +snp_rs10954365 snp_rs10954365 1 chr7 131855009 131855207 - CCCTCTCCTTTCAGTTTACATCATGGTCCCTGGAGATGGCAGAAAGAAGTGCCAAGTGCCGGGATTTATGACCTCCTTCCACCCTTCTGTGTCTTGGGGCTTTGTGAAGCTCCTTATCCTCACAGGGTCCCTCATGGGGATTATAAC Homo sapiens hg19 +snp_rs11118109 snp_rs11118109 1 chr1 218632773 218632961 - GCAAGAACAATCAAGGGCCCGCACTGTGCTGACACAATGCTAGCAAAATTGTCACATTACCTTACACAGAGAGGGCCTTTCCGTTTATATGGAATCCTTACCAAACCCCTTGACATAGGCAGTGCTTATTAGCTTT Homo sapiens hg19 +snp_rs10168253 snp_rs10168253 1 chr2 180659424 180659615 - TGTTTAAGGACCAATTTCTTCTCTTTAATACCTAATCAGATCCTGCTCAGCGGTGTCCCCATCTCATCCAAGATGACTCCTGAAGTCACATTGATCCCTCTTTCCTCTATTATGATTGCAGATTCAAGGTAACTAGG Homo sapiens hg19 +snp_rs11118515 snp_rs11118515 1 chr1 220473871 220474090 - TTGTTTTCTTTTCTGTCTCCTGAAAGAGCTGTGCTCCAGTGTCTGCCCGGTAAAGTTGCTAGTGGCAGCATTCCTGGAAGCTCCTTGCTCCAGATGATGTCAGACCTCATGTGACCCAACCATCGCACGCCCGGAAACATTACATCATTCTAAGATGTGATTCCTTTTA Homo sapiens hg19 +snp_rs10133359 snp_rs10133359 1 chr14 26718991 26719190 - ACTGAAAAATTCATCTTTACATTTCCCACCTACCTTACCAAATGAAAGAATTACTAACTATTCCAAATGCAAGTTTGTTTTATTTCCTTTTTCACAGCAAAATCAGTCTATTATAATAATTATTTTATAAATGTCTCTTTTTTTTT Homo sapiens hg19 +snp_rs1038024 snp_rs1038024 1 chr17 25725450 25725643 - TCGCACACAGCTGGTGGGCTTCTGGGCTTCCTAACCATAGGCTTCCATTTTCCCCCATTCAAGTGAGACCATCTTGGTCCACCTGACTTGTCTGAGCCACCTCCTGGCATTAGGTTCCTGGTCCTCATGCCACTGTCACC Homo sapiens hg19 +snp_rs11144978 snp_rs11144978 1 chr9 79225176 79225367 - GCATGGAGATCAGTGATAAAGTTGGGAGCCTAATTAAAAATCAAAATCATAAGGGGCCTTTTATAAGCTGAAGTTAAAAATAAATAAAATGAAGACAACTTCAGTCGTGGAAGCCAAGACTTTCAGTCATAGATTACAG Homo sapiens hg19 +snp_rs10932037 snp_rs10932037 1 chr2 204825190 204825397 - AATGAATATTCTGCTCTACCCCATGAGAATGCTGGCCCATTAAAGATGATTTTGTTTGCAATTTTAATATGATCTACAAAAAGAACTAAACTTGTAATTAATAGCACCATGAAAACATAGATAATGGTAGAAAATAGGATAATAAAATAAATTT Homo sapiens hg19 +snp_rs11114607 snp_rs11114607 1 chr12 81157287 81157492 - ACTTGACACACGTAAAGAAAGTAAAGGTTGCGAGCTACCATGACAATCTATGGACACAGGCTTCCTTACAAGTTCTCTTTAGTCACAGCAAAGCAAGCTGAAAAAAAGAAGTTGGTTTTCAGTTTAATTTAGTGTGTATAAATGTCAATAAA Homo sapiens hg19 +snp_rs10058793 snp_rs10058793 1 chr5 4739659 4739860 - TATTCAGGGAATAAATAGAAACAAGGCCACCATGATAATGTTGTCGGTTCAGAGAGAGAGAGAGAGAGAATATACACATACACATATACATACACACACATATATTCATACATACACATAGTACAAACTATATCATGAATAGAAA Homo sapiens hg19 +snp_rs11017093 snp_rs11017093 1 chr10 131925950 131926165 - TGTATTTGTGGAGGCTCCACCGACTCACCCAAAACACGTGCTTTTCCCCTGACCTGCAAACTTTTAACACCTTCTTCTCTTCCCGTTTCACTAGGCTATTTGAGATCCTGCAAGATTTATCAAGACTGTACTAGCCATATGAAAGCATGTTAACACAGGGAGGG Homo sapiens hg19 +snp_rs1015077 snp_rs1015077 1 chr6 167526356 167526573 - ACATAATGCAAAATTACAACAAGTGCATCCGAGATTGTTATACAAATGGAATCGCAGTATTGTTAAATGACATAAATGCATTCACCCACAACACAGTGAAACTGATTGTCACTGGTTTATCACTTTCACTTGGGAGACAATGCTATCACTAGAACTCCTTCT Homo sapiens hg19 +snp_rs12785223 snp_rs12785223 1 chr10 104843861 104844061 - TAAAAGACTGCAAATGCCACGGTTAAATAAATTCAGTGGAGACTATAAATGGACCAGTCAAGAGGCTAAATTTTCAGAGCACGATCCTCTTTGGAATGTAAAATAGAGACTAAAAGTGGAGAGAAAAGGGATTCCAAAAAGATGTGG Homo sapiens hg19 +snp_rs10745558 snp_rs10745558 1 chr12 91910025 91910223 - CCAAGCTAAGCCAAAGTTAGGAATCTAGGAAAAAACTCCCAAAAGATGAACCAAGCTGACATCCATTTTTAGTAAGTAAAAATAACATGATTCATAGGCAAATGAGTATAAAGGTCCCGAGTTTCTGCCTGCTGCTTCTTAATT Homo sapiens hg19 +snp_rs10499441 snp_rs10499441 1 chr7 14505532 14505753 - TTTTTATGTTTATGATCCCTGGAAGTAGATGTACACTTGAAATGTTTAGGATTTATATGATAATTCCCCCTCCCTGTTGATGGCTCATTTCTGTTCTTAGGCCAGCTTGTGTGCACATGCAAACGTCTACTTCCAACTCATGCAAATCCGATGGATAATGCATCACA Homo sapiens hg19 +snp_rs11137287 snp_rs11137287 1 chr9 140382556 140382764 - GGAAAAATAAAAATAAATCCACATCAGAGAGCCACGTTCGGGCCGAAGCTCGGGACGAGACATCAGACCGCGAGAGCCGCGTTCGGGCCGAAGCTCGGGACGAGACATCAGACTGCAAGTGAAGCTCGGGACGAGACATCAGACCACGAGAGCAGCG Homo sapiens hg19 +snp_rs10489858 snp_rs10489858 1 chr1 19947099 19947295 - CCGTACCACTCAATCAAAAAGATGAGCAATGCTTCCACATCCATCAATATCAAGTAGAAAATCTTAATCTCTAGAATTCAGATATATGCCCAACCACCCAGTTTTGCTCCTATTATAGGCATTTATCTGCAAGTATAAATAT Homo sapiens hg19 +snp_rs10519980 snp_rs10519980 1 chr4 149634856 149635064 - AGAGACTCCCTCGTTGACCTGCTTGAGTGCCCCGTTTGAGAAGGTGCTCTCTTTATGCTAAAGAAGGACTGGATGTAGCAAAAAGGTTTCTGTGCTGAGAGCCAGAAAGTTGCCCTTGAAGTATCAGCAATGAAGGAAGAGCTAATTTTTTTTTT Homo sapiens hg19 +snp_rs10489924 snp_rs10489924 1 chr1 99458822 99459029 - TCTTCTCTCTGGCTCCTTATCACATGAATACTTGGGGTTCCCTTTTTATTTTTCCTGGGCTAAATCTAGAATACAGATATGAGAATCCAGTAGACACTTTTTTCAAGCCACACTATCAGGCTCTTTCTGTCATCCCATTTTTGGAAAAGATTC Homo sapiens hg19 +snp_rs11081675 snp_rs11081675 1 chr18 28580528 28580717 - ACGGTGAGAATAGCTAAAGAAGAGGAAAACAGCATAGCCTACAAGACAGGAGATGATAAAGTTTAGGGGCTATTTAGCAAATAATAAATAAATTGATTTAGAATAGAAGAAATCATGTGTTGGAAAAGAGGCTTGAA Homo sapiens hg19 +snp_rs10183112 snp_rs10183112 1 chr2 38445612 38445817 - AGGAAACCATCAGCCAGAGGCACAACCACAGCCATTGTCTGCTGTTCCCTGCCAAACCTCCACCTTTCCTCTGTCATCTTCATCTCTGATTCCCCAGAGGACCCGTCTCTGACTACCAGACCTCAGCGCTCCCTGGGAAAGGCCCCCAGGGAG Homo sapiens hg19 +snp_rs10817727 snp_rs10817727 1 chr9 117979260 117979455 - TGTTTTCTCCTCTCACTATAAGGATGTGGCCCAACTTCCAAGGGTGCCCCACCATTGAGGTCTTCACTGCCAGGAACTGAAATCTCATGGGACACAAAACCCACCTACACATCCTCTCAACTTCTCCTTTCTGTGTTGAGTC Homo sapiens hg19 +snp_rs10440685 snp_rs10440685 1 chr5 77182925 77183128 - AGGGGTTAAGTCTTCGCATTGTGAGGTTCTATTGACTTTTCCTGCAGGCTTGCCCTTTATCCTTGTCTGTATTTTAGTTTTTAAGAAGCCTTCAAAAGGTAGGGCACTCATTAGTGGTTCCATAGTGGATGGTTATGTTCAGTTGTTAT Homo sapiens hg19 +snp_rs10486239 snp_rs10486239 1 chr7 8584076 8584285 - ATGACACCATCATCTGCCTCAGTACGGTCTACATTATAACATTGCACTGCACTCCTAACTTCACTATTCTTTTGTTTATGGCATATGCCTATGATGTCTTCGGGTAGGGATCATTTCAAATGCCAAGCATCCTTCCATGTAAACATTCTTTAT Homo sapiens hg19 +snp_rs10505770 snp_rs10505770 1 chr12 13025899 13026105 - GAGTCAGTGTGAGCTGTATGGTGTCTACTCTTCCCTCTGTGGTTCTTCAAAGGGAGTAGAGGGTGGGTGATGGGGGTGACTCAAGAATGCATAGGACTTTATCAATCAAATTCCCATACGGAATCAGAACAAGCCTGGCAGGTTCATGGACCA Homo sapiens hg19 +snp_rs10223664 snp_rs10223664 1 chr6 98677548 98677736 - ATTCCCATGACCTCAACCAACCTCCAGTCACCACTAATTTTCACATATATGTCTTTGGTTCTTATCATTCTCCTAAGATCTACACTTCTAATTACATTGAAAATAATTATATGTGCATATTCTATATGTTCTATAA Homo sapiens hg19 +snp_rs10490026 snp_rs10490026 1 chr2 210733280 210733489 - GGTTGTCCAGTTGAAACTACAAAAAGTCTAATGAATGTCATTGCACAGCATGGGAGTCTCTTACAGTCTACAGGTAGAAAACATCAGGAGTCTGGCTACTTTCCTTGACTTCTTTGCCATTTTTTCCTTGAATTTTATAAGATCATTATGTATAT Homo sapiens hg19 +snp_rs10514527 snp_rs10514527 1 chr16 82137489 82137696 - TCGTCAGTGAAAATTTCTTGCCTGAACATTTAAGCCTTACCAAAAAACCCTACCCAGGCCAAGAACAGCATGTTTCTATTTAGAACCTTCTCTATGTGGAATTAGTTCACCTCTGACAGTCAGGAGACAGAGCACAGGGCAATGCTAAAGAGAGG Homo sapiens hg19 +snp_rs10744146 snp_rs10744146 1 chr12 17212724 17212922 - CACTTCAGTGATTGCTCCTTTGTGTTCATTCAACTCATGCTGCATCAAAATACAGGCCTCTTGGCTCTAACGCATGGTTCTAGCTCTTTGGGTACTAATACTGACTTTCTTCTGCCTCAATTTGTCAATTATCATTCAAATTTGT Homo sapiens hg19 +snp_rs10845745 snp_rs10845745 1 chr12 13466200 13466390 - AATAAATGCATGTTGCAGGATAATACCACATGATTCAGGGACAAACTTCTCTCCTCCAGCTGCTCCTCTGACACAGTCTTAGACCTCTCTTATCATTGGTCTACCATTTATTTAGCAATTTTTATTGAAAGCCTTCTA Homo sapiens hg19 +snp_rs1032886 snp_rs1032886 1 chr12 44528902 44529101 - TTTTCTAGTAATTTATTCCTGCCATTGGGGTAAGCTTATGGAGACATATACAATGATGCCCAACTCTGCTATTGTTTCCTTTTCTGGTAATTTAGAACCAATACAAAAAGAGAGAAAGAAGGAAATATCTTTCCTGGAGGTTATAT Homo sapiens hg19 +snp_rs10487449 snp_rs10487449 1 chr7 126071915 126072127 - ATGAATTACAACCTGTTTCTAGAACAGTTATCAAATCTTCTTGGCTTTGGGAAATAGATTTAGGTTGGGGAATACTCTTTGGGTAAATTCAAGTTAGTGTCAACTTTTTATTTGACAGTTTTCATTTTTATTGATTTGTCCATAATATGAAGTTTGTAGT Homo sapiens hg19 +snp_rs10813205 snp_rs10813205 1 chr9 29943479 29943701 - CAAATTTCATATTGAAAGCAATGGTGATATTTTCTATCTTCTGGTTTTTGATGGATGTGTAAATTTCAAGACCTCCATCACGATTGCCAGGCAAGGCATATATATACTTAGGGCAATTCCATTTCCTAGATTTGGCAGGTTATTGAAAGGAATTTGTTGAGAAATTT Homo sapiens hg19 +snp_rs1003346 snp_rs1003346 1 chr9 111815176 111815380 - CCTGCCTTTACCCAGTTTCTCCTCTTTAAGCCTGACATATAAATTAAACCACTTTACTTTAAGGATTTAGTTAATATTCTAGAAATGTTTCTTCCTCTATTTTCTCCAGTTGATTCCCTTTCTTTTTTTCTTTCAAATAGGAAAGGTTACTT Homo sapiens hg19 +snp_rs11185125 snp_rs11185125 1 chr1 108061495 108061685 - AAATGTGTTAGGGAGGCTTCCAAGGTAAGGAAGCAGTAAATAAAGGCACAAAGATGGGAAAATGTGGAGCATATAGTAGAAATAAGAATTATATTAATAACAATTGTATGTTTAAAACAAGGTTCATGAAGGCATG Homo sapiens hg19 +snp_rs11073674 snp_rs11073674 1 chr15 87361824 87362022 - TATGCTGAGCCACGATGTTGTACTACTGGCCTGCAAGTATTTATTCCAGAAATGCATTTTCCCCTTTGTCAACTCCCACTATCACCATCCACTTTGGTCATTCACACCTTCTCTTTCCTGGACAAGTTTTCACCAAATCCATCTA Homo sapiens hg19 +snp_rs10187631 snp_rs10187631 1 chr2 120343679 120343887 - GGCAGGTTATTGGGTCCCCTTGCAGCAGCAGGAAGTCAAGTGCTTCCTTTCAAGTGACCCAGCCACTCCCTGCATTCCTGATATTTTTGCACCCCTCCCTTCTCGTTAAGCCACCAGCCAGCTTCATCTTTGACTCTGTACATCTCTTCTCTACCCC Homo sapiens hg19 +snp_rs11125812 snp_rs11125812 1 chr2 59989457 59989672 - GCACCATCCATGGTAATGGAGCAGAGAGGGATGCCCTGTGCTATTGGTAGAAAAGACAAAATGTGAAATAGAATGAAAATTGCCTCCAGTCACTTAATTTGGAGGCAGCACAGGAGCTGTGCAGCATTTCAGTCGGATGGTACCTTGAATTAAAAGAACTAA Homo sapiens hg19 +snp_rs10837327 snp_rs10837327 1 chr11 40082638 40082845 - TCTTCTAGAAAATTTTCCCACTATCAACAATAGTCCCAAATTGTCAGCATAATACTCCCACACTCTCACCATAACCTGTCTACTCAGTTTTGCTCTCATCAGATTGTAATCATATTTTTATGGTACATGTATCGTTTGTCTTGACCAACATATTATA Homo sapiens hg19 +snp_rs10937470 snp_rs10937470 1 chr3 191000655 191000854 - ACAAGTAAATGCCAAGATCGGAGGTCATTATACTATAACATCACTGGAGCCATAAAATTGAAATTGGAGATATACTGAAAGACTTTGACTTAAAAAGAAAACCAGCACAATTAAAGCAAGTATTAAAGAGAGTAACTGATGGGA Homo sapiens hg19 +snp_rs10510060 snp_rs10510060 1 chr10 121863321 121863513 - CAAGTTCCAGATGTAGCGAATCTCTGCCTGTGTGGACAAAGAGACACATTCAGAGGTGAGCCCAGAGGGGGTAAAGTGGACTGGGGAGAACTTCGGAGGATGTTCATGTCCAGGAGCAGCCCCACGCCCTGTATGGTCGG Homo sapiens hg19 +snp_rs10871565 snp_rs10871565 1 chr18 75698200 75698390 - AGAAGAGGGCTACTACAGCAGAATGGCAGAGAGATGCCTCTGCAGCAACAGAACGAATACTTGCTTTAAAAAAAATGTCAAAATGTGGATGTGCCTCCAATCATTTAAAAAATAGAAGGTGATAAGTTGAAAATGTC Homo sapiens hg19 +snp_rs10950049 snp_rs10950049 1 chr7 66230706 66230897 - CATAACCTCCCATGTTATCAGGAAACTGTCCTCTCAATCCACAAAGATAAGCTGGCAGCAGCTATATTTGTATAAGGTGAATGGTCCCCCAATTCAGGATCACAGCTGATTGCCTCCAACTGTGTTAGAGTCTTTTGCTT Homo sapiens hg19 +snp_rs10816943 snp_rs10816943 1 chr9 112983665 112983860 - GCAGTTGAGGACAAATTAAAACTTCCATGAGGCTCAACGTCCAGCAAACATCTAACTTAATTCCACTTCTCAAAGTTCCTTTAGTTCTTGGGCTTACCACATCTCCAAATCCACCAAAAGACAAACATAGCCAATTAGAATAT Homo sapiens hg19 +snp_rs10512393 snp_rs10512393 1 chr9 112153006 112153198 - TGTTTCTAATTCAATCGTCCACATGCCCCTGTACTGAGTGGCTTCCATTCAGGTGTTTGTTTTTGCCAGTGATGAAACTGTCTATTTCTCTCCATGTAATGAGTGTCATCCTGCCTTAAAAAAAAAATGAGAAAAATAA Homo sapiens hg19 +snp_rs10511942 snp_rs10511942 1 chr9 37702718 37702918 - CAACAAAGAATGACCTCGAAGACTCTACATCAAAAAGTATTGTGGGCCTAAAAGCTTCAGACATACAAAGAAACACAATCTAGAAAATACCCTTCCAGAGCACTGTGTAAGCTATGGTTTACCCTTCCTAAGTGAGAACTAGAATTA Homo sapiens hg19 +snp_rs10240790 snp_rs10240790 1 chr7 89880793 89880985 - GGGAATAACAATGTCCTCACCTCATGCAGCTATTGGTCTGGCATGGGATTTTATAGAAGGCTTTGTATGTAACACAAGGATCTTAAAAAGCCATTGAATGGTTTGAGACTGAACATATAAACAAAACTGGTCAGACTATAT Homo sapiens hg19 +snp_rs1147199 snp_rs1147199 1 chr9 87275738 87275942 - AATCCAAATAATGTTCATCATCAGACACTTCATTTTCCCAAGAATGTCTGTATTTTAGTGGAGGACACTGGGAAAAAGATGTAATCCAAAGGAATTTCAGGTACCATGGCAACCATAAAAGAGGGAGTATTTGAGCATGGAGGACTCAACAC Homo sapiens hg19 +snp_rs1058326 snp_rs1058326 1 chr9 27446918 27447133 - ACAAGCTTTTCCTTCAACGAACCTTTGTAGGCATAAGGACGTGTGTTATCTGCAAAGGTCTCTGCAGACAGGACCTTTGGGTGTTATATCTTAAAAAAAAAATTCATGCTAATTTCCTATTCTAGTGAATAATTCTGTCCATATTTTCTTTCACATAATCAT Homo sapiens hg19 +snp_rs10484820 snp_rs10484820 1 chr6 139858111 139858344 - GCGGATAGAGTTTTGGTTTGAACATGCGACTACCCTGATTCCACATTCAGGCGTTTTGTCATGAATTCACCGAGGGACTGTTGGTCCAGGCCTCTGTAGGCAAATTATATTTGCCAATAGATGACATTTATAGTGTAACTGGATATCCCTGGATGAGAAGCTAAAAATGAAAAAGTAAATA Homo sapiens hg19 +snp_rs10829531 snp_rs10829531 1 chr10 130761792 130761989 - AGAGAACTAGGGCAGGCAAGAGCAGCTCACACATGCCTTCCCCACCATTGCAGATGGGATGCATCTTCATGTCTCACTAAGATGCTGATTAGTTTTCAAGGTTAATAAAATTATGGGTTTTGAGTCTGAAATCTTCATGTACAGT Homo sapiens hg19 +snp_rs10835211 snp_rs10835211 1 chr11 27701208 27701403 - TCAACTGAGCGACCAGAGCTCTGCTGGTGAAACAGGAACTTGTATTGTGCCCCTGACGTGCACCTTGAAGGTGTCAGCTCATTGTCCCTTTGTTCACATAAATAGTTTTTTAAGAATTGTTTTTGATCTTGTGAGCCTCTAA Homo sapiens hg19 +snp_rs10160742 snp_rs10160742 1 chr11 115239233 115239435 - TGTTAACCCAAAGATGGATAGGAAAACAAAAATATGCTACAAGGAAAATTATTATGGGCTATTCAGGTGTTCTTGTTACTGTATGTGCCCCTAATATTAGGATTTTCTTCACAGAACATTATCATTCAAAAAAGAAGTCATTACATATA Homo sapiens hg19 +snp_rs10512461 snp_rs10512461 1 chr17 32475233 32475435 - ATCTTCCAGTTTAGAACTTTAAGCTGTAAGCTCTCTGGAAGTCGTGCTTTCAGGGGTATATAAAATTCTTTCTGATGTGATGAAGGGGTAAGACAATGACTGAGAGCTGACTATTTTGATGACCCACAATGTCTACTTGCAAAGAAAAA Homo sapiens hg19 +snp_rs10869031 snp_rs10869031 1 chr9 74130136 74130327 - TGTCCAGTCATTAGACCAGCCCACTCTTTCTCACTCCCTGTAGTCCTAAAAACAGTTCTTAAATATCCTTCTGTTTGAAAAATTCCCATCTGCTCCACCCACGATCACAGCAGAATGAAGACATCGCGTTCCTCTGTT Homo sapiens hg19 +snp_rs1055010 snp_rs1055010 1 chr7 29550950 29551166 - AGGCACTATGCCTGACTAAACAAGATGGCTGGCAAACCCACTATGATAAAGATACAGTATTATTGGCATTTAAGGTTCAGCTGAAAGGTGTCAGCATTTTTCTGGTAGTGGTACTTTGCCTTCCAAACTGTAACAACTGGATATTGATCACAATAAGTATTTTA Homo sapiens hg19 +snp_rs10930486 snp_rs10930486 1 chr2 172472416 172472622 - CCCTCTTCATTGAAAGAAAGCTACTACACCGATCCCTTGGGTTGTTTTGTGTGCGTGCATGTGTGTGTTTATCTTTAAATATTTAGGGAGTACAAGTGCAGATGTCTCACATGCATCTATCGTGTCATGGTGAAGTCTTGGCTTTTAGTGTAT Homo sapiens hg19 +snp_rs1052448 snp_rs1052448 1 chr9 18927860 18928079 - CTGATTTTGAAAAATAGTAATTTAGAAATTACACAGTACTTTTAAAAGCAGACAACTGAGAATTATTTGTTGGACAAAAAAGAATTCCCTAAAATGACAAAAAACAAAAAACAAAAAACCTTCACCACTTCCAGAGCACTTGAATAAAATGAGAATCACTTGACTCA Homo sapiens hg19 +snp_rs10488735 snp_rs10488735 1 chr11 34438404 34438596 - TCTGGCATTAAGGTTCTCTCTATCCAGTGATGCAATAGACAGTTGCTGGTTTTGCAACTCTATGCACTCTACATTTTGTAATATCATCCTAATTTTGCTTTGTAGAGTTATTCCCTCCTCTACTCTACCTTTTATTTACA Homo sapiens hg19 +snp_rs10255854 snp_rs10255854 1 chr7 38959675 38959892 - GAGTTTCTCCAGTAATTTCCAGACGTTTATGTGTCAGAGAAGAAGTTCATGATACATCAGCTGGAGATGTTAGGCCTTGGGTTCTGGTACTGCCACATAAGTATTTTTCTCCAGCAGTTGTCAAACCAGTTAGAAATATTACCCAGGAGTCTAACAATGATGCTCT Homo sapiens hg19 +snp_rs10961084 snp_rs10961084 1 chr9 13484879 13485076 - AGCGTGTTGGTAGAGCCTATGTGGTTGATGCTATTTCACAGGACTTAGTTATAGAAGAGGAAGGTTTACCTTCATTTTAAATTAATGCAAATGGTGCAGATTCAGCCCCAGTCAACTGGTATTTTCCAGATTCATAGTTTACTTT Homo sapiens hg19 +snp_rs10189774 snp_rs10189774 1 chr2 171375347 171375538 - AAACAGGGAATAATTCCAGGAGTAACCTATTTCCACATTTTGATTGAGGACAGTTTATTGATGAGTTTCTCAACAATGAGGGTAACAAATACAATTCTTTCTTCCAGTGACCATGGCTAATCAATCACGGCCTTCTTT Homo sapiens hg19 +snp_rs10893306 snp_rs10893306 1 chr11 124813366 124813553 - AGGGATGGTGTCGTCTATTACTTTTGAATGTGCCGCCTTCCTCCTCTTCCACATCCCACCACTTTTATTAATGTTTGGAACATAGAGTGTTCTTCACACAGTAGGCAATTATCAGATGCTGGCCAGCTGATTCCC Homo sapiens hg19 +snp_rs1106944 snp_rs1106944 1 chr11 126008119 126008321 - CATGTTATAAAACCATAGGCAAACCAAAGTCACGAAGAGAGAAAGGCTGAGCCAAGAGACCACAGCCCAGGAGGAGAGAGAATGACGAGGCCGGGTACTTTGCTTAATTAAAGTCTCATATCCCTCATAGTTATCTCTACATCCACTTT Homo sapiens hg19 +snp_rs1055352 snp_rs1055352 1 chr9 128910268 128910455 - ATGGTGTAAAAACACAGATTTGTCCCACCTGGTTTCACCCCACTTTCCTCTCTGGTCCCAGGCCTCAGGGTCTGGACATTTCTGCCAGGGAACATCTGTTCTGCAGAGCAGCCAGGACTCCCCCTGCCACCCCCCA Homo sapiens hg19 +snp_rs10141526 snp_rs10141526 1 chr14 62303100 62303301 - GGAAAATGAGGGACTGGGGAAGGAATGTAGGAGAATGGCTACAGGATTTCAGAAGGTGCACATTTAATATTCAATTTTAGACTGTTTATGTTACCAAGATATAAACTTCTCCTATCCCTCCAAACCATCAATTGGTTTTCTACATATT Homo sapiens hg19 +snp_rs10094093 snp_rs10094093 1 chr8 4505761 4505952 - GCACCATTAGGGGCCACTTGGTGACAGACAATCCCGTAGATCACAGAGAATGTGGATCATGTCATTATATCCTAAGTGACTCACAGGTGGGGAAGCAGGAACAAGATAAACAAAAAACTACAAGAAATTAGCAAGAAAAA Homo sapiens hg19 +snp_rs11009888 snp_rs11009888 1 chr10 35007947 35008138 - GCTTTTTTCAGACAGGTCTAAAAAGGGCTCTGCCCTAGTCTATCCCTAGCAGAGATGTTACATGTGCCTGGCTCAATTCAACGTATCAGTATATTGTGGGGAGAAAGGATGAATAAGGACAACACCACAAGTTGTGAT Homo sapiens hg19 +snp_rs11082351 snp_rs11082351 1 chr18 41484188 41484382 - GGGAATCCCAATAGAAGAAGGTAAAGGTGATGCTGTTCTCAACCAAATTAAAACTTCAATGCTTCTCTGAAGTAGGAAAAAGGCCTTCTAGAGTATGTAATCTTTTAAAACTTTTTGAACATCAAAGAGGTCTCAGAAAAT Homo sapiens hg19 +snp_rs1113272 snp_rs1113272 1 chr4 165646618 165646832 - GATTCAAATAGTTCTTTCTTCTCTGTAGCCTTGACTTCAGGTTTGACTGGCTCAGGTGACGTCTCACTATTCTGTTTAGTGAATAGTGTTGTCCAGCCTGTTGTCCAGCCTGCAATGCATACATCTCACTATTCTGTTTAGTGAATAGTGTTGTCCAGCCTG Homo sapiens hg19 +snp_rs10250461 snp_rs10250461 1 chr7 22289201 22289407 - GGTGTTTTATAAACGGTGTTTGGTGGTCTAAGAAACCAGTCACCATAGAATAAAACATATATGTTATAGTTCTGCGACTACCTTATTTATTGGAGAATTGCCTAACTTTCTGTGTTTCTCTACCAGTGAAAGCTTTATAAAAGGAGAATTATT Homo sapiens hg19 +snp_rs11143230 snp_rs11143230 1 chr9 74887553 74887757 - TAGATTTCCAAGCCTTGACTCTTAACATCTGTCATGGAACCATTATAGCACCATCTGCCCAATTTCCCCGCTGATGATTTCACCTGACTATGTAATCCTGGAAGAGGGGTGATGCCCATTAACTTGTAGTTGGTTTATATAAGCTAGAGCA Homo sapiens hg19 +snp_rs10520689 snp_rs10520689 1 chr15 90950208 90950408 - GGGAGTGGTTCCTCAGCTTCTACGTTGAAAAGGATTCTGATCTATCAGCAGTGCTTGCTGTGGGTGTAAAATAACCTACCACAAATCTAACATCCTTGCTCTAGACTACGAGATCCATCTTAAAGTATGGCCTCCAGAACTAAACAC Homo sapiens hg19 +snp_rs11079784 snp_rs11079784 1 chr17 45702116 45702318 - GCTATTTGAAAAACAAAACATCTGACACAGAAAAGGCTGAATTAAAACCTTTAGAGACCCAAAGCAGCAGGGCTATTGTGCCCAAATCACTCAAGGTATTGGTAGGAAAGAACACAAACTGAGGAAGGTTTAATAAAGGACTATTTACAG Homo sapiens hg19 +snp_rs11632663 snp_rs11632663 1 chr15 27564636 27564822 - TGGACACCCTCTTATCCAGCCTCGTCCAGTCCTCTCCATCCTCCTGTCTGCCATCTTCCCGTGGCATTGGCATATTTGCCAACAGCCTGCCCCTCCTCATGGTATTACTCACTATTTTTTCTCCTTATGTTAACA Homo sapiens hg19 +snp_rs10079889 snp_rs10079889 1 chr5 32975335 32975532 - AAAATCTAGAATACTTTACCTTGCGTTTTAGATACATGTAGACACATCTTATCCTACTCAACAAACCCTGCTCCATCCCCAAAATGCTCCCACTTCGCTGTAAATTTTTAAAGTACTGGGATTTTTTTCTGCTTATCTTTGCAT Homo sapiens hg19 +snp_rs10504373 snp_rs10504373 1 chr8 65107774 65107977 - AGTTCTCTTTAGGGCAATCATTGTAGTACCTTCCACATTTCTATTGCACTTAAACATAAGTTCTTGATGTGCTCTACAGCTCTGGATCACAATTTAAACATAATATTTACTCTATCTCAGATACGGCCTCTTTAAAACCACAACTTTT Homo sapiens hg19 +snp_rs1160382 snp_rs1160382 1 chr7 149279842 149280037 - TTGTGAACATTTGTAGAGCTGTGAAGATGGAAATCTCTTAGCACTGGAAGTCCTTAGCATTGGAAGCACATTGTCATGGTGTTTGACATTCCTGGGGACAAAAGGAGAAGGTGGTGAGGAAAATAGGATTGTTATTCTGTCGT Homo sapiens hg19 +snp_rs10887788 snp_rs10887788 1 chr10 89898602 89898802 - ACTAACAAAAGACAAACAGGGCAGTCTCCATGAAGATGTCTGGGCATGCAAATAATTCTGGTTTTGATGTAATTATCAGACTCCTAGCACTGAAGGAGAGATGGTTGGAGAATTCTATAGTACTTCCAGCTTATCTGCATAGTTTAT Homo sapiens hg19 +snp_rs10257539 snp_rs10257539 1 chr7 135439746 135439954 - GATCTTAGGTGTCTTGTTAGCTAAGGGAGAAAACCCAGAAGAGTTCTGTCACTGTGTCCGTATGTCCCTCCAATGATGGGAATACCCCAATCCACAAGTGACTCTTCTCTCCAAAAAGAATTTCTGCCATCTGCCATCCCCACAGCTGCAGGCCAC Homo sapiens hg19 +snp_rs11002633 snp_rs11002633 1 chr10 80447619 80447825 - CACTATTGCTTGCATGGGCTGACACTTGTGAAGTGATATCAGAAATATTGTTAGTGACATTTTTATTTGGAATTTTAAAAGAAGAAATTGACATCTCCTTCCTTAAAAGGCTACAAGAGTATCTTCAACCCTGACATCTTAAATGTTTATTTTT Homo sapiens hg19 +snp_rs1058932 snp_rs1058932 1 chr10 96796712 96796899 - CATCTGGCTGCCGATCTGCTATCACCTGCAACTCTTTTTTTATCAAGGACATTCCCACTATTATGTCTTCTCTGACCTCTCATCAAATCTTCCCATTCACTCAATATCCCATAAGCATCCAAACTCCATTAAGGA Homo sapiens hg19 +snp_rs11063356 snp_rs11063356 1 chr12 4938444 4938642 - CCTCTATATTTAGCGAGCAATAAGAGCAATGTGGACACGTTATGCCAGTGAAAAGTTTGTCGATTAGCTCCTTTTCTACTGGATAATCATATCCAGCAATGCTTCTGGACAGCACAGGCAAATCAGCTCAAGGAGGGGAAGCACCCTC Homo sapiens hg19 +snp_rs1016726 snp_rs1016726 1 chr7 29356254 29356442 - AGACTCCATACTCTAGAAAGCTTAGCTATTTCTTTGGCAAATTAGAAGTATAATCCCAACATTGTGGAAAAAAAAAAATCACACATCTTTGTATGAATTCAGTAAATGTTGATGTCACATTGGGGGCAGCAGCTCT Homo sapiens hg19 +snp_rs10875815 snp_rs10875815 1 chr12 48834175 48834367 - GACCATGAGAGAGCTAATGGCAGAGGAAGGACTGGGCAGAGCCTGTGGCAAACTTCAAAAAGAAACCAGAAACATTTAACAAAGACCCTTTAGATGATGAAACACAATTGGAGGATTAATGAGAACTATATTTGAGGGA Homo sapiens hg19 +snp_rs10957982 snp_rs10957982 1 chr8 81455607 81455809 - ACTGGTTTAGAGTAATTCAATTTAGCTGTCATTTAATCCAGACCAAAAAAAGCCATTCACCTTGTTTAGCTGCCGCAACTGACTCATGTGTCAAGGAACTCAGAAATCCAACTTAGAGATCACAGGTCAACCTGTGCAAAGCTTGCGGC Homo sapiens hg19 +snp_rs1258540 snp_rs1258540 1 chr7 63109119 63109314 - GGGACTCTCCTTCAGCATCAAGCTGCCACCCTCAGATGTGGTCCCCTGCACCTCCCTCCACAGGCTGGCCCCTGCCTGCCTCCTCACCTCACATCTCCCCAGTCACCTCCTCTGCTCCAAGGCATGGCAGGTTCCTGCCCTTCT Homo sapiens hg19 +snp_rs10087078 snp_rs10087078 1 chr8 8930587 8930780 - TAAGATACTGCCTTCTGCAAAGATAAATAATGTTGATTCACTGCGCTTCCAAAATCAAGGACAAAGCCGAAGGCATGAGGCCAGGTGATAAAGTTTATGGCTGAGAAGGCAACCAAGATTCAAACTGACTGACAGCAGAA Homo sapiens hg19 +snp_rs1050190 snp_rs1050190 1 chr3 141644656 141644852 - ATAAAAAGAGGACAAGACCCCCATCCTACATGTTTGGAATCAGGTGTTCACCGGTCCCTATCTGGCGACTGTACACTGGTTCAAAGGGCAGCAGAGGCAACAGGCAGTTACTTCAGAGGACACTGAACACTATGATCTGGAA Homo sapiens hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/TSACP/tobed.pl Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,37 @@ +#!/usr/bin/perl -w +# + +my $mani = shift || "TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; +open M, "<$mani"; + +my %probes = (); +while (<M>) { + if (/\[Probes\]/) { readline(M); last; } +} + +while (<M>) { + if (/\[Targets\]/) { + readline(M); + last; + } + my @row = split(/\t/, $_); + $probes{$row[2]} = [@row]; + #print STDERR join(":", @row[2, 9, 11]) . "\n"; sleep 1; + +} + +while (<M>) { + my @row = split(/\t/, $_); + #print join("\t", @row[3, 4,5]) . "\n"; + my $ori = $probes{$row[0]}->[13]; + my $oriT = $row[6]; + my $s = $row[4] + length($probes{$row[0]}->[9]); + my $e = $row[5] - length($probes{$row[1]}->[11]); + if ($oriT eq "+") { + $s = $row[4] + length($probes{$row[1]}->[11]); + $e = $row[5] - length($probes{$row[0]}->[9]); + } + $row[4]--; + $s--; + print join("\t", @row[3, 4, 5], $row[0], 100, $oriT, $s, $e) . "\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/TSACP/truseq_amplicon_cancer_panel_manifest_afp1_pn15032433_b.txt Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,449 @@ +[Header] +Customer Name "ILLUMINA, INC." +Product Type 15032433 +Date Manufactured 25/10/2012 +Lot 35105 +DesignStudio ID NA +Target Plexity 212 + +[Probes] +Target Region Name Target Region ID Target ID Species Build ID Chromosome Start Position End Position Submitted Target Region Strand ULSO Sequence ULSO Genomic Hits DLSO Sequence DLSO Genomic Hits Probe Strand Designer Design Score Expected Amplifed Region Size SNP Masking Labels +MPL1_2 MPL1_2.chr1.43815008.43815009 MPL1_2.chr1.43815008.43815009_tile_1 Homo sapiens hg19 chr1 43815008 43815009 - AAGTGGCGAAGCCGTAGGTGCGCACG 0 TCAGCAGCAGCAGGCCCAGGACGG 0 - ILLUMINA NA 183 TRUE +NRAS1_7 NRAS1_7.chr1.115256528.115256531 NRAS1_7.chr1.115256528.115256531_tile_1 Homo sapiens hg19 chr1 115256528 115256531 - CAATAGCATTGCATTCCCTGTGGTTTT 0 AGAGTACAGTGCCATGAGAGACCAAT 0 - ILLUMINA NA 182 TRUE +NRAS8_13 NRAS8_13.chr1.115258730.115258748 NRAS8_13.chr1.115258730.115258748_tile_1 Homo sapiens hg19 chr1 115258730 115258748 - GGGTTTTCATTTCCATTGATTATAGAAAG 0 CTGACAATCCAGCTAATCCAGAACCA 0 - ILLUMINA NA 184 TRUE +ALK1 ALK1.chr2.29432664.29432664 ALK1.chr2.29432664.29432664_tile_1 Homo sapiens hg19 chr2 29432664 29432664 - GATAAAATCCTAGTGATGGCCGTTGTA 0 GACATCTACAGGTGAGTAAAGACTGCC 0 - ILLUMINA NA 188 TRUE +ALK2 ALK2.chr2.29443695.29443695 ALK2.chr2.29443695.29443695_tile_1 Homo sapiens hg19 chr2 29443695 29443695 - TGCTGCCCATGTTTACAGAATGCCTT 0 CACCAGAACATTGTTCGCTGCATTG 0 - ILLUMINA NA 171 TRUE +IDH1_1_2 IDH1_1_2.chr2.209113112.209113113 IDH1_1_2.chr2.209113112.209113113_tile_1 Homo sapiens hg19 chr2 209113112 209113113 - GAGGGTTGAGGAGTTCAAGTTGAAACA 0 CATGCTTATGGGGATCAAGTAAGTCAT 0 - ILLUMINA NA 182 TRUE +ERBB4_1_2 ERBB4_1_2.chr2.212288942.212288955 ERBB4_1_2.chr2.212288942.212288955_tile_1 Homo sapiens hg19 chr2 212288942 212288955 - ACTACTGGTATAGTGCTGGTTTGTTCA 0 AGAACGTTTGCCTCAGCCTCCCATCTG 0 - ILLUMINA NA 190 TRUE +ERBB4_3_4 ERBB4_3_4.chr2.212530066.212530135 ERBB4_3_4.chr2.212530066.212530135_tile_1 Homo sapiens hg19 chr2 212530066 212530135 - CATTTCAGGGTCCTGACAACTGTACAA 0 AACTGCACCCAAGGGTAAGCATTCTT 0 - ILLUMINA NA 176 TRUE +ERBB4_5 ERBB4_5.chr2.212576857.212576857 ERBB4_5.chr2.212576857.212576857_tile_1 Homo sapiens hg19 chr2 212576857 212576857 - ATACTCTGCTATTTTATAATGAAGATGCAA 0 CCAGTAACATTGACAAATTCATAAACTGTA 0 - ILLUMINA NA 171 TRUE +ERBB4_6_7 ERBB4_6_7.chr2.212578341.212578349 ERBB4_6_7.chr2.212578341.212578349_tile_1 Homo sapiens hg19 chr2 212578341 212578349 - AGGGTAAGATACATAAACACTATCAATGA 0 TGCCTGCCCTAGTTCCAAGATGGAA 0 - ILLUMINA NA 186 TRUE +ERBB4_8 ERBB4_8.chr2.212587147.212587147 ERBB4_8.chr2.212587147.212587147_tile_1 Homo sapiens hg19 chr2 212587147 212587147 - TGAAAGTAATATTTGCTGTGTTGCAGG 0 CATTCTGTGTCAAGAAATGTCCACGTA 0 - ILLUMINA NA 172 TRUE +ERBB4_9 ERBB4_9.chr2.212589811.212589811 ERBB4_9.chr2.212589811.212589811_tile_1 Homo sapiens hg19 chr2 212589811 212589811 - GCAGACTTTGATCATGGTCCTATCTCT 0 GACTGCTTTGTATGTCTGTGATTTCTC 0 - ILLUMINA NA 176 TRUE +ERBB4_10 ERBB4_10.chr2.212652764.212652764 ERBB4_10.chr2.212652764.212652764_tile_1 Homo sapiens hg19 chr2 212652764 212652764 - AATGGTGGAGTCTATGTAGACCAGAAC 0 TCTTTTTAATTTCTCAAAATGTTCTACCCT 0 - ILLUMINA NA 172 TRUE +ERBB4_11 ERBB4_11.chr2.212812157.212812157 ERBB4_11.chr2.212812157.212812157_tile_1 Homo sapiens hg19 chr2 212812157 212812157 - GTGGCTCTTAATCAGTTTCGTTACCTG 0 GGTAAGGAATATATCCAAAATGGCAAATA 0 - ILLUMINA NA 186 TRUE +VHL1_2 VHL1_2.chr3.10183797.10183817 VHL1_2.chr3.10183797.10183817_tile_1 Homo sapiens hg19 chr3 10183797 10183817 - AAAATGGACCCCGGGGCGGTAGAGGG 0 ATACGGGCAGCACGACGCGCGGACT 0 - ILLUMINA NA 185 TRUE +VHL3_5 VHL3_5.chr3.10188245.10188301 VHL3_5.chr3.10188245.10188301_tile_1 Homo sapiens hg19 chr3 10188245 10188301 - GAACTGGGCTTAATTTTTCAAGTGGTC 0 AGAAGCCCATCGTGTGTCCCTGCATCT 0 - ILLUMINA NA 186 TRUE +VHL6_8 VHL6_8.chr3.10191480.10191506 VHL6_8.chr3.10191480.10191506_tile_1 Homo sapiens hg19 chr3 10191480 10191506 - TTGATGTGCAATGCGCTCCTGTGTCAG 0 GTATACACTGGAAGGGCAAAAACCAAAT 0 - ILLUMINA NA 186 TRUE +MLH1 MLH1.chr3.37067240.37067240 MLH1.chr3.37067240.37067240_tile_1 Homo sapiens hg19 chr3 37067240 37067240 - TGGGAGTTCAAGCATCTCCTCATCTTG 0 ATCTGGTGGGCATAGACCTTATCACT 0 - ILLUMINA NA 184 TRUE +CTNNB1_1_16 CTNNB1_1_16.chr3.41266040.41266137 CTNNB1_1_16.chr3.41266040.41266137_tile_1 Homo sapiens hg19 chr3 41266040 41266137 - GGTATCCACATCCTCTTCCTCAGGATT 0 GTCCAACTCCATCAAATCAGCTATAAA 0 - ILLUMINA NA 172 TRUE +PIK3CA1 PIK3CA1.chr3.178916876.178916876 PIK3CA1.chr3.178916876.178916876_tile_1 Homo sapiens hg19 chr3 178916876 178916876 - AGGGACAACAGTTAAGCTTTATGGTTA 0 AAAAATTCTTCCCTTTCTGCTTCTTG 0 - ILLUMINA NA 190 TRUE +PIK3CA2 PIK3CA2.chr3.178921553.178921553 PIK3CA2.chr3.178921553.178921553_tile_1 Homo sapiens hg19 chr3 178921553 178921553 - ACATTCGGAGATTTGGATGTTCTCCTA 0 TCACGTAGGTTGCACAAAGAATTTTTA 0 - ILLUMINA NA 186 TRUE +PIK3CA3 PIK3CA3.chr3.178927980.178927980 PIK3CA3.chr3.178927980.178927980_tile_1 Homo sapiens hg19 chr3 178927980 178927980 - CTTCTAATCCATGAGGTACTGGCCAAA 0 AACACATTTCAAAACACTTTTCTTCCC 0 - ILLUMINA NA 178 TRUE +PIK3CA4_11 PIK3CA4_11.chr3.178936074.178936095 PIK3CA4_11.chr3.178936074.178936095_tile_1 Homo sapiens hg19 chr3 178936074 178936095 - GGTATGGTAAAAACATGCTGAGATCAG 0 CTCGTGTAGAAATTGCTTTGAGCTGTT 0 - ILLUMINA NA 172 TRUE +PIK3CA12 PIK3CA12.chr3.178938860.178938860 PIK3CA12.chr3.178938860.178938860_tile_1 Homo sapiens hg19 chr3 178938860 178938860 - TAAACAACTCTGCCCCACTGCAGTGAA 0 CTTCAAATACATCCCACATGCACGACA 0 - ILLUMINA NA 174 TRUE +PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_1 Homo sapiens hg19 chr3 178952007 178952150 - CCAAAGCCTCTTGCTCAGTTTTATCTAA 0 AGCCTTGTAACACATCTCCTGAAACC 0 - ILLUMINA NA 175 TRUE +PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_2 Homo sapiens hg19 chr3 178952007 178952150 + CATTGCATACATTCGAAAGACCCTAGC 0 AGATAACTGAGAAAATGAAAGCTCACTCTG 0 + ILLUMINA NA 187 TRUE +FGFR3_1_2 FGFR3_1_2.chr4.1803564.1803568 FGFR3_1_2.chr4.1803564.1803568_tile_1 Homo sapiens hg19 chr4 1803564 1803568 - TTGCTGCCATTCACCTCCACGTGCTTG 0 TCTGTGGGGGCAGATGACGCTCAGG 0 - ILLUMINA NA 176 TRUE +FGFR3_3_4 FGFR3_3_4.chr4.1806119.1806153 FGFR3_3_4.chr4.1806119.1806153_tile_1 Homo sapiens hg19 chr4 1806119 1806153 - GCTCAGAACCTGGTATCTACTTTCTGT 0 TAGCTGAGGATGCCTGCATACACACTG 0 - ILLUMINA NA 188 TRUE +FGFR3_5_7 FGFR3_5_7.chr4.1807862.1807890 FGFR3_5_7.chr4.1807862.1807890_tile_1 Homo sapiens hg19 chr4 1807862 1807890 - AAACAAGGCCTCAGGCGCCATCCACT 0 GCCAGCCCGAAGTCTGCGATCT 0 - ILLUMINA NA 191 TRUE +FGFR3_8 FGFR3_8.chr4.1808331.1808331 FGFR3_8.chr4.1808331.1808331_tile_1 Homo sapiens hg19 chr4 1808331 1808331 - CCGGAGGGACCCCCACCCCTGA 0 CCCCCAGCGTGAAGATCTCCCA 0 - ILLUMINA NA 171 TRUE +FGFR3_9 FGFR3_9.chr4.1808949.1808949 FGFR3_9.chr4.1808949.1808949_tile_1 Homo sapiens hg19 chr4 1808949 1808949 - AAGCTCTGTGTAGCTGTCTCTCCATCT 0 TCGTGGGCAAACACGGAGTCGTC 0 - ILLUMINA NA 186 TRUE +PDGFRA1_4 PDGFRA1_4.chr4.55141013.55141049 PDGFRA1_4.chr4.55141013.55141049_tile_1 Homo sapiens hg19 chr4 55141013 55141049 - TACCCCATGGAACTTACCAAGCACTAG 0 CTATAAATGACCAGGACAGGTAACTGG 0 - ILLUMINA NA 178 TRUE +PDGFRA5 PDGFRA5.chr4.55144146.55144146 PDGFRA5.chr4.55144146.55144146_tile_1 Homo sapiens hg19 chr4 55144146 55144146 - GTCAGCTCCATTCAAGGGACTTCTATT 0 TACAATGTTCAAATGTGGCCCCAGGT 0 - ILLUMINA NA 188 TRUE +PDGFRA6 PDGFRA6.chr4.55144547.55144547 PDGFRA6.chr4.55144547.55144547_tile_1 Homo sapiens hg19 chr4 55144547 55144547 - AACATCTCTCTTTGCACCCACCTCCGT 0 ATGATGTAAATGGGGCCTATGGGGAC 0 - ILLUMINA NA 186 TRUE +PDGFRA7_23 PDGFRA7_23.chr4.55152040.55152109 PDGFRA7_23.chr4.55152040.55152109_tile_1 Homo sapiens hg19 chr4 55152040 55152109 - AGAGATTAAAGTGAAGGAGGATGAGCC 0 TTGCGAGCAGCCAGATCACGGTGGA 0 - ILLUMINA NA 174 TRUE +KIT1 KIT1.chr4.55561764.55561764 KIT1.chr4.55561764.55561764_tile_1 Homo sapiens hg19 chr4 55561764 55561764 - GTGTTTGTTGGTGCACGTGTATTTGC 0 CCCACGCGGACTATTAAGTCTGATTTT 0 - ILLUMINA NA 179 TRUE +KIT2 KIT2.chr4.55592185.55592186 KIT2.chr4.55592185.55592186_tile_1 Homo sapiens hg19 chr4 55592185 55592186 - CAGTATGGTGTGATGCATGTATTACCA 0 CAGAAGTCTTGCCCACATCGTTGTAA 0 - ILLUMINA NA 188 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_1 Homo sapiens hg19 chr4 55593464 55593689 - GAGAGAACAAATAAATGGTTACCTGTAAA 0 GTGGAATCACAAACTTTGGCAGGA 0 - ILLUMINA NA 172 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_2 Homo sapiens hg19 chr4 55593464 55593689 + CGTAGCTGGCATGATGTGCATTATTG 0 ACCCATGTATGAAGTACAGTGGAAGG 0 + ILLUMINA NA 175 TRUE +KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_3 Homo sapiens hg19 chr4 55593464 55593689 - GTGACATGGAAAGCCCCTGTTTCATA 0 TCTGTGGGGAGAAAGGGAAAAATAGAT 0 - ILLUMINA NA 185 TRUE +KIT20_21 KIT20_21.chr4.55594221.55594258 KIT20_21.chr4.55594221.55594258_tile_1 Homo sapiens hg19 chr4 55594221 55594258 - GCAGTTTATAATCTAGCATTGCCAAAAT 0 AGTTCAGACATGAGGGCTTCCCGTTCT 0 - ILLUMINA NA 189 TRUE +KIT22 KIT22.chr4.55595519.55595519 KIT22.chr4.55595519.55595519_tile_1 Homo sapiens hg19 chr4 55595519 55595519 - ACTATTTATGTAAATCAGTCTTACCAGGA 0 TAATGACCAGGGTGGGCCCTAAAAGC 0 - ILLUMINA NA 184 TRUE +KIT23 KIT23.chr4.55597495.55597497 KIT23.chr4.55597495.55597497_tile_1 Homo sapiens hg19 chr4 55597495 55597497 - CCACATTAGCATGATATACATACTCTCT 0 CTGGGAGAGATGAAACAAGTCATGACT 0 - ILLUMINA NA 187 TRUE +KIT24_28 KIT24_28.chr4.55599320.55599348 KIT24_28.chr4.55599320.55599348_tile_1 Homo sapiens hg19 chr4 55599320 55599348 - TGTGTGATATCCCTAGACAGGATTTAC 0 GGCTAGACCAAAATCACAAATCTTTGT 0 - ILLUMINA NA 184 TRUE +KIT29 KIT29.chr4.55602694.55602694 KIT29.chr4.55602694.55602694_tile_1 Homo sapiens hg19 chr4 55602694 55602694 - GAAGCAGGACACCAATGAAACTTCAAG 0 TGCCATCCACTTCACAGGTAGTCGA 0 - ILLUMINA NA 186 TRUE +KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_1 Homo sapiens hg19 chr4 55946114 55946257 - ATTCTCCAGCCTGACTCGGGGACCACACTG 0 CATTTGATTTTCATTTCGACAACAGAAAAA 0 - ILLUMINA NA 173 TRUE +KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_2 Homo sapiens hg19 chr4 55946114 55946257 + ATGCTTCCTTTTAAACAGGAGGAGAGC 0 GGACTGGTAGCCGCTTGTCTGGTTTGA 0 + ILLUMINA NA 188 TRUE +KDR3 KDR3.chr4.55953807.55953807 KDR3.chr4.55953807.55953807_tile_1 Homo sapiens hg19 chr4 55953807 55953807 - CTGAAGCCATAACAACAGTCTTCTGTG 0 ATTCCATTATGACAACACAGCAGGAAT 0 - ILLUMINA NA 190 TRUE +KDR4 KDR4.chr4.55955111.55955127 KDR4.chr4.55955111.55955127_tile_1 Homo sapiens hg19 chr4 55955111 55955127 - TCCTTATTTAGCATCTCACCTCGTCAG 0 AGCCCAGTCAGAGACCCACGTTTT 0 - ILLUMINA NA 174 TRUE +KDR6 KDR6.chr4.55960989.55961023 KDR6.chr4.55960989.55961023_tile_1 Homo sapiens hg19 chr4 55960989 55961023 - TTTATAGACCAAAGGGGCACGATTCCG 0 TGTAGAAGAAGAGGAAGGTACTGGCTA 0 - ILLUMINA NA 172 TRUE +KDR8 KDR8.chr4.55962507.55962507 KDR8.chr4.55962507.55962507_tile_1 Homo sapiens hg19 chr4 55962507 55962507 - GGAAATGCATGTGGTCTGTAAACTAGG 0 AACACACAGTGAGCATCGAGCTCTCA 0 - ILLUMINA NA 178 TRUE +KDR9 KDR9.chr4.55972964.55972964 KDR9.chr4.55972964.55972964_tile_1 Homo sapiens hg19 chr4 55972964 55972964 - TACCATGGTAGGCTGCGTTGGAAGTTA 0 GACAAACCCATACCCTTGTGAAGAATG 0 - ILLUMINA NA 172 TRUE +KDR10 KDR10.chr4.55979623.55979623 KDR10.chr4.55979623.55979623_tile_1 Homo sapiens hg19 chr4 55979623 55979623 - CTGGTGTCCCTGTTTTTAGCATTAAAT 0 ACCTAAAAACCCAGTCTGGGAGTGAG 0 - ILLUMINA NA 182 TRUE +KDR11 KDR11.chr4.55980348.55980348 KDR11.chr4.55980348.55980348_tile_1 Homo sapiens hg19 chr4 55980348 55980348 - TCTGTGCAAAGTTATAGGCTTATTTGC 0 AGAACTGAACTAAATGTGGGGATTGAC 0 - ILLUMINA NA 178 TRUE +FBXW7_1 FBXW7_1.chr4.153245446.153245446 FBXW7_1.chr4.153245446.153245446_tile_1 Homo sapiens hg19 chr4 153245446 153245446 - CAGTAATTGATAGGAAGAGTATCCATACT 0 AACAAGTGGAATGGAACTCAAAGACAA 0 - ILLUMINA NA 190 TRUE +FBXW7_2 FBXW7_2.chr4.153247288.153247366 FBXW7_2.chr4.153247288.153247366_tile_1 Homo sapiens hg19 chr4 153247288 153247366 - GTTTTGTTTTGTTTTTCTGTTTCTCCCT 0 TATGATGGCAGGAGGGTTGTTAGTGGAGCA 0 - ILLUMINA NA 171 TRUE +FBXW7_5 FBXW7_5.chr4.153249384.153249384 FBXW7_5.chr4.153249384.153249384_tile_1 Homo sapiens hg19 chr4 153249384 153249384 - CATACAGGTGGAGTATGGTCATCACAA 0 AAAAGGTAAGGGAAAATCTTGTCATGG 0 - ILLUMINA NA 184 TRUE +FBXW7_7 FBXW7_7.chr4.153250883.153250883 FBXW7_7.chr4.153250883.153250883_tile_1 Homo sapiens hg19 chr4 153250883 153250883 - CTGTTCCTGTTTATGCCTTCATTTTTC 0 AGTTAGTGGTTCTGATGACAACACTT 0 - ILLUMINA NA 180 TRUE +FBXW7_8 FBXW7_8.chr4.153258983.153258983 FBXW7_8.chr4.153258983.153258983_tile_1 Homo sapiens hg19 chr4 153258983 153258983 - CTGTAATTTGGGACATCTGTTAAAACAATA 0 GACTTCATTTCATTGCTCCCTAAAGAGG 0 - ILLUMINA NA 191 TRUE +APC1 APC1.chr5.112173917.112173917 APC1.chr5.112173917.112173917_tile_1 Homo sapiens hg19 chr5 112173917 112173917 - GCAGAGCTTCTTCTAAGTGCATTTCTC 0 TGAAGAAGTTCCTGGATTTTCTGTTGC 0 - ILLUMINA NA 186 TRUE +APC2 APC2.chr5.112174631.112174631 APC2.chr5.112174631.112174631_tile_1 Homo sapiens hg19 chr5 112174631 112174631 - AATTTGTTGGTCTCTCTTCTTCTTCAT 0 TTTGTTTCTGAACCATTGGCTCCCCGT 0 - ILLUMINA NA 174 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_1 Homo sapiens hg19 chr5 112175162 112175958 + CTTGCAAAGTTTCTTCTATTAACCAAGA 0 TTCTGCTAATACCCTGCAAATAGCAGA 0 + ILLUMINA NA 176 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_2 Homo sapiens hg19 chr5 112175162 112175958 - TGCTGGATTTGGTTCTAGGGTGCT 0 CCTATTTCATCTTCAGCTGATGACAAA 0 - ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_3 Homo sapiens hg19 chr5 112175162 112175958 + GAAAAGATTGGAACTAGGTCAGCTGAAG 0 AGCGAAATCTCCCTCCAAAAGTGGT 0 + ILLUMINA NA 172 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_4 Homo sapiens hg19 chr5 112175162 112175958 - CTATCAAGTGAACTGACAGAAGTACATC 0 CCTGGCTGATTCTGAAGATAAACTAGAACC 0 - ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_5 Homo sapiens hg19 chr5 112175162 112175958 + CACCCAAAAGTCCACCTGAACACTAT 0 ATTATAAGCCCCAGTGATCTTCCAGAT 0 + ILLUMINA NA 174 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_6 Homo sapiens hg19 chr5 112175162 112175958 - CTCTCTCTTTTCAGCAGTAGGTGCTT 0 CACTTACCATTCCACTGCATGGTTCA 0 - ILLUMINA NA 173 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_7 Homo sapiens hg19 chr5 112175162 112175958 + CAAACCAAGCGAGAAGTACCTAAAAAT 0 AAAGTACTCCAGATGGATTTTCTTGTTC 0 + ILLUMINA NA 171 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_8 Homo sapiens hg19 chr5 112175162 112175958 - CTCTGATTCTGTTTCATTCCCATTGTCATT 0 GTGGCAAAATGTAATAAAGTATCAGCATCT 0 - ILLUMINA NA 173 TRUE +APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_9 Homo sapiens hg19 chr5 112175162 112175958 + ATTAAGAATAATGCCTCCAGTTCAGGA 0 AGAAGAATGTATTATTTCTGCCATGCC 0 + ILLUMINA NA 190 TRUE +CSF1R1_3 CSF1R1_3.chr5.149433644.149433646 CSF1R1_3.chr5.149433644.149433646_tile_1 Homo sapiens hg19 chr5 149433644 149433646 - TCCCACCCTCAGGACTATACCAATCT 0 AGTTCTGCTGAGGAGTTGACGACAGGG 0 - ILLUMINA NA 185 TRUE +CSF1R4 CSF1R4.chr5.149453044.149453044 CSF1R4.chr5.149453044.149453044_tile_1 Homo sapiens hg19 chr5 149453044 149453044 - TCTTGGGTGGTGGGGACTATGTACCT 0 AACTTGAGCTCTGAGCAGAACCTCATC 0 - ILLUMINA NA 175 TRUE +NPM1 NPM1.chr5.170837547.170837548 NPM1.chr5.170837547.170837548_tile_1 Homo sapiens hg19 chr5 170837547 170837548 - GGTAGGGAAAGTTCTCACTCTGCATTA 0 AAAAAGAAATGTGGTTAAGGAACCAC 0 - ILLUMINA NA 186 TRUE +EGFR1 EGFR1.chr7.55211080.55211080 EGFR1.chr7.55211080.55211080_tile_1 Homo sapiens hg19 chr7 55211080 55211080 - CATCGGAACTGCTGTCTGCATTTATGA 0 GATGATCTGCAGGTTTTCCAAAGGAAT 0 - ILLUMINA NA 188 TRUE +EGFR2 EGFR2.chr7.55221822.55221822 EGFR2.chr7.55221822.55221822_tile_1 Homo sapiens hg19 chr7 55221822 55221822 - AAGCAAGGCAAACACATCCACCCAAAG 0 AAAGCTGTATTTGCCCTCGGGGTTCA 0 - ILLUMINA NA 174 TRUE +EGFR3 EGFR3.chr7.55233043.55233043 EGFR3.chr7.55233043.55233043_tile_1 Homo sapiens hg19 chr7 55233043 55233043 - AACTTGGGAGACATTTTTGATCTCTGA 0 TGCCGGGCAGGTCTTGACGCAGT 0 - ILLUMINA NA 186 TRUE +EGFR4 EGFR4.chr7.55241677.55241708 EGFR4.chr7.55241677.55241708_tile_1 Homo sapiens hg19 chr7 55241677 55241708 - GGAAATATACAGCTTGCAAGGACTCTG 0 TCAAGATCCTCAAGAGAGCTTGGTTG 0 - ILLUMINA NA 180 TRUE +EGFR9 EGFR9.chr7.55242418.55242511 EGFR9.chr7.55242418.55242511_tile_1 Homo sapiens hg19 chr7 55242418 55242511 - ATGAGAAAAGGTGGGCCTGAGGTTCAG 0 CCTATGACAGAGAGAGAAGGAAGACGTT 0 - ILLUMINA NA 190 TRUE +EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_1 Homo sapiens hg19 chr7 55249005 55249131 - AGGTGAGGCAGATGCCCAGCAGGCGG 0 CGCATGAATGCGATCTTGAGTTTCAA 0 - ILLUMINA NA 175 TRUE +EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_2 Homo sapiens hg19 chr7 55249005 55249131 + CAGCGTGGACAACCCCCACGTGT 0 GTGTGTGCAGATCGCAAAGGTAATCA 0 + ILLUMINA NA 177 TRUE +EGFR54 EGFR54.chr7.55259514.55259524 EGFR54.chr7.55259514.55259524_tile_1 Homo sapiens hg19 chr7 55259514 55259524 - CCTCCCCTGCATGTGTTAAACAATACA 0 CCAAAATCTGTGATCTTGACATGCTGC 0 - ILLUMINA NA 178 TRUE +MET1 MET1.chr7.116339642.116339642 MET1.chr7.116339642.116339642_tile_1 Homo sapiens hg19 chr7 116339642 116339642 - CCTTCTCACTGATATCGAATGCAATGG 0 CTTCTATCTGTGGGGAGAATATGCAGT 0 - ILLUMINA NA 180 TRUE +MET2 MET2.chr7.116340262.116340262 MET2.chr7.116340262.116340262_tile_1 Homo sapiens hg19 chr7 116340262 116340262 - GCCCTGGATATTCTTTTTGAGACTGAT 0 GAAGAAGTCGTTGACATATTTGATAGG 0 - ILLUMINA NA 188 TRUE +MET3 MET3.chr7.116411990.116411990 MET3.chr7.116411990.116411990_tile_1 Homo sapiens hg19 chr7 116411990 116411990 - TGCAAAACCAAAAATAAACAACAATGTC 0 TTACACTTCGGGCACTTACAAGCCTA 0 - ILLUMINA NA 171 TRUE +MET4 MET4.chr7.116417463.116417464 MET4.chr7.116417463.116417464_tile_1 Homo sapiens hg19 chr7 116417463 116417464 - CACAAGGGGAAAGTGTAAATCAACGTTT 0 CACAACCAAAATGCCCTGTGCAAAAGA 0 - ILLUMINA NA 191 TRUE +MET6 MET6.chr7.116423413.116423474 MET6.chr7.116423413.116423474_tile_1 Homo sapiens hg19 chr7 116423413 116423474 - GAGGAGAAACTCAGAGATAACCAATAC 0 TGTCTCTGGCAAGACCAAAATCAGCA 0 - ILLUMINA NA 172 TRUE +SMO1 SMO1.chr7.128845101.128845101 SMO1.chr7.128845101.128845101_tile_1 Homo sapiens hg19 chr7 128845101 128845101 - TGACCAGGGTGAAGAGCGTGCAGAG 0 AAGGGCACTTCGCACTGGCCTGAA 0 - ILLUMINA NA 186 TRUE +SMO2 SMO2.chr7.128846040.128846040 SMO2.chr7.128846040.128846040_tile_1 Homo sapiens hg19 chr7 128846040 128846040 - ATTGCCACAGTGAGGACAAAGGGGAGT 0 GTACACGATGACAAAGATGATGACGCA 0 - ILLUMINA NA 186 TRUE +SMO3 SMO3.chr7.128846374.128846374 SMO3.chr7.128846374.128846374_tile_1 Homo sapiens hg19 chr7 128846374 128846374 - TAGCTGGGGTTTCAGCATGGGGGCAGC 0 AAGCCCGCACGGTATCGGTAGTTCT 0 - ILLUMINA NA 190 TRUE +SMO4 SMO4.chr7.128850341.128850341 SMO4.chr7.128850341.128850341_tile_1 Homo sapiens hg19 chr7 128850341 128850341 - AACCACTGACCAAGGCTGTGCTAGAGG 0 TCATGGCGATGCCAGTTCCAAACA 0 - ILLUMINA NA 190 TRUE +SMO5 SMO5.chr7.128851593.128851593 SMO5.chr7.128851593.128851593_tile_1 Homo sapiens hg19 chr7 128851593 128851593 - TTCAGATCCTCTGGGGCCTTTCCTTC 0 AGAAATATCCTGGGGCAGTATGGCTCC 0 - ILLUMINA NA 173 TRUE +BRAF1 BRAF1.chr7.140453121.140453193 BRAF1.chr7.140453121.140453193_tile_1 Homo sapiens hg19 chr7 140453121 140453193 - ACCTAAACTCTTCATAATGCTTGCTCT 0 GGTCCCATCAGTTTGAACAGTTGTCT 0 - ILLUMINA NA 176 TRUE +BRAF28 BRAF28.chr7.140481397.140481478 BRAF28.chr7.140481397.140481478_tile_1 Homo sapiens hg19 chr7 140481397 140481478 - GGTTTTCTTTTTCTGTTTGGCTTGACT 0 CTACAAGGGAAAGTGGCATGGTAAGTA 0 - ILLUMINA NA 178 TRUE +FGFR1_1 FGFR1_1.chr8.38282209.38282209 FGFR1_1.chr8.38282209.38282209_tile_1 Homo sapiens hg19 chr8 38282209 38282209 - TTTTGAGAGGCTTGGGCTCAGCAGAA 0 TCACCGGCCCATCCTGCAAGCAGGG 0 - ILLUMINA NA 179 TRUE +FGFR1_2 FGFR1_2.chr8.38285938.38285938 FGFR1_2.chr8.38285938.38285938_tile_1 Homo sapiens hg19 chr8 38285938 38285938 - AAGAGATCATCACTAAGGGAGCAGTGG 0 GGATGATGATGATGATGATGACTCCTC 0 - ILLUMINA NA 184 TRUE +JAK2_1 JAK2_1.chr9.5073769.5073770 JAK2_1.chr9.5073769.5073770_tile_1 Homo sapiens hg19 chr9 5073769 5073770 - TTCAGTTTCAAAAATACTTAACTCCTGTT 0 CTCCATAATTTAAAACCAAATGCTTGTG 0 - ILLUMINA NA 188 TRUE +CDKN2A1 CDKN2A1.chr9.21971153.21971187 CDKN2A1.chr9.21971153.21971187_tile_1 Homo sapiens hg19 chr9 21971153 21971187 - TTGTGTGGGGGTCTGCTTGGCGGTGA 0 AACTGCGCCGACCCCGCCACTCTCA 0 - ILLUMINA NA 187 TRUE +ABL1_1 ABL1_1.chr9.133738330.133738364 ABL1_1.chr9.133738330.133738364_tile_1 Homo sapiens hg19 chr9 133738330 133738364 - ATGCATCGCCTAATGCCAGCAGACGC 0 TGATGTCCGTGCGTTCCATCTCCCAC 0 - ILLUMINA NA 191 TRUE +ABL1_9 ABL1_9.chr9.133747520.133747520 ABL1_9.chr9.133747520.133747520_tile_1 Homo sapiens hg19 chr9 133747520 133747520 - AGCGCCTGTGTCACCCTGGGGGT 0 AAAACGAAGGTGAAATTATTTCAGGAA 0 - ILLUMINA NA 190 TRUE +ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_1 Homo sapiens hg19 chr9 133748283 133748414 + AGAATCCTTCAGAAGGCTTTTTCTTTAGAC 0 AACCTCCTGGACTACCTGAGGGAGT 0 + ILLUMINA NA 172 TRUE +ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_2 Homo sapiens hg19 chr9 133748283 133748414 - TCCATGGCGCAGGCTGCCTGGCC 0 CCGTAGGTCATGAACTCAGTGATGA 0 - ILLUMINA NA 182 TRUE +ABL1_16 ABL1_16.chr9.133750356.133750356 ABL1_16.chr9.133750356.133750356_tile_1 Homo sapiens hg19 chr9 133750356 133750356 - GGGAAGAGCAAGAAAGAGGCAGAAAAA 0 TGTGTAGGTGTCCCCTGTCATCAA 0 - ILLUMINA NA 190 TRUE +NOTCH1_1 NOTCH1_1.chr9.139397768.139397768 NOTCH1_1.chr9.139397768.139397768_tile_1 Homo sapiens hg19 chr9 139397768 139397768 - AGACCTGGCTTCCCACCACCCCAGGCT 0 AGATTGACAACCGGCAGTGTGTGCAG 0 - ILLUMINA NA 190 TRUE +NOTCH1_2 NOTCH1_2.chr9.139399344.139399422 NOTCH1_2.chr9.139399344.139399422_tile_1 Homo sapiens hg19 chr9 139399344 139399422 - AGTGCGAGTGGGACGGGCTGGACTGT 0 ACACCAACGTGGTCTTCAAGCGTGAC 0 - ILLUMINA NA 171 TRUE +RET1 RET1.chr10.43609078.43609104 RET1.chr10.43609078.43609104_tile_1 Homo sapiens hg19 chr10 43609078 43609104 - ACTCGCCTCCCAGCAATTTCCTCCC 0 TTGCAGGTGCCATAGCCAGCTTTAAT 0 - ILLUMINA NA 180 TRUE +RET2_9 RET2_9.chr10.43609940.43609950 RET2_9.chr10.43609940.43609950_tile_1 Homo sapiens hg19 chr10 43609940 43609950 + AAGCCTCACACCACCCCCACCCACAGAT 0 CCCATCTCCTCAGCTGAGATGACCTT 0 + ILLUMINA NA 175 TRUE +RET10 RET10.chr10.43613840.43613840 RET10.chr10.43613840.43613840_tile_1 Homo sapiens hg19 chr10 43613840 43613840 - AGAACAGGGCTGTATGGAGCCCCCAGC 0 GGGAGGCGTTCTCTGAAATGCAG 0 - ILLUMINA NA 190 TRUE +RET11_12 RET11_12.chr10.43615567.43615569 RET11_12.chr10.43615567.43615569_tile_1 Homo sapiens hg19 chr10 43615567 43615569 - ATGGTGCACCTGGGATCCCTGGGAG 0 ATGTTTCTGGCTGCCAAGTCCCGATGAA 0 - ILLUMINA NA 172 TRUE +RET13 RET13.chr10.43617416.43617416 RET13.chr10.43617416.43617416_tile_1 Homo sapiens hg19 chr10 43617416 43617416 - AATTCCCTGGCCAAGCTGCACAGACGG 0 CCATTTAACTGGAATCCGACCCTAAAG 0 - ILLUMINA NA 178 TRUE +PTEN1 PTEN1.chr10.89624242.89624244 PTEN1.chr10.89624242.89624244_tile_1 Homo sapiens hg19 chr10 89624242 89624244 - TACGGACATTTTCGCATCCGTCTACTC 0 ATGATGGCTGTCATGTCTGGGAGCCTG 0 - ILLUMINA NA 176 TRUE +PTEN3 PTEN3.chr10.89685307.89685307 PTEN3.chr10.89685307.89685307_tile_1 Homo sapiens hg19 chr10 89685307 89685307 - TGGACTTCTTGACTTAATCGGTTTAGG 0 CTTGTAATGGTTTTTATGCTTTGAATCCA 0 - ILLUMINA NA 186 TRUE +PTEN4 PTEN4.chr10.89711893.89711900 PTEN4.chr10.89711893.89711900_tile_1 Homo sapiens hg19 chr10 89711893 89711900 - GGATGAGAATTTCAAGCACTTACTGCA 0 TGGGAATAGTTACTCCCTGGTGGACA 0 - ILLUMINA NA 176 TRUE +PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_1 Homo sapiens hg19 chr10 89717615 89717772 - GGGTCCTGAATTGGAGGAATATATCTTCAC 0 ACACGAAATATGGATTCTGTATCTGC 0 - ILLUMINA NA 181 TRUE +PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_2 Homo sapiens hg19 chr10 89717615 89717772 + CAGTTTGTGGTCTGCCAGCTAAA 0 AAAGGTTTGTACTTTACTTTCATTGGGAG 0 + ILLUMINA NA 188 TRUE +PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_1 Homo sapiens hg19 chr10 89720716 89720852 - AATTTGGAGAAAAGTATCGGTTGGCTT 0 AGGTTTCCTCTGGTCCTGGTATGAA 0 - ILLUMINA NA 188 TRUE +PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_2 Homo sapiens hg19 chr10 89720716 89720852 + AAAATGATCTTGACAAAGCAAATAAAGAC 0 CTTGCTTGACAAGTTTTTAACTTATGTATT 0 + ILLUMINA NA 179 TRUE +FGFR2_1 FGFR2_1.chr10.123258034.123258034 FGFR2_1.chr10.123258034.123258034_tile_1 Homo sapiens hg19 chr10 123258034 123258034 - CTAACAGTAGCTGCCCATGAGTTAGAG 0 TTCTTGGAGCCTGCACACAGGATGGTG 0 - ILLUMINA NA 180 TRUE +FGFR2_2 FGFR2_2.chr10.123274774.123274803 FGFR2_2.chr10.123274774.123274803_tile_1 Homo sapiens hg19 chr10 123274774 123274803 - GCCTTTTGGTTCCTTTGGTTGTGCTAT 0 CATAGGGGTCTTCTTAATCGCCTGTAT 0 - ILLUMINA NA 186 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_1 Homo sapiens hg19 chr10 123279503 123279677 - CACGTGGAAAAGAACGGCAGTAAATAC 0 GGAGTTGAGAGAGGATGATTCTCTTTT 0 - ILLUMINA NA 172 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_2 Homo sapiens hg19 chr10 123279503 123279677 + TTTAGATTCAGAAAGTCCTCACCTTGAG 0 CTCCTCCGACCACTGTGGAGGCATTT 0 + ILLUMINA NA 171 TRUE +FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_3 Homo sapiens hg19 chr10 123279503 123279677 - ACTGACAGCCCTCTGGACAACACAGCT 0 CGTAGAGTTTGTCTGCAAGGTTTACAG 0 - ILLUMINA NA 184 TRUE +HRAS1 HRAS1.chr11.533873.533875 HRAS1.chr11.533873.533875_tile_1 Homo sapiens hg19 chr11 533873 533875 - TACCAGGGAGAGGCTGGCTGTGTGAAC 0 AGTACAGCGCCATGCGGGACCAGTAC 0 - ILLUMINA NA 180 TRUE +HRAS6 HRAS6.chr11.534285.534289 HRAS6.chr11.534285.534289_tile_1 Homo sapiens hg19 chr11 534285 534289 - CTGCCCTGTGGGGCCTGGGGCTGG 0 AAGAGTGCGCTGACCATCCAGCTGATC 0 - ILLUMINA NA 185 TRUE +ATM1 ATM1.chr11.108117847.108117848 ATM1.chr11.108117847.108117848_tile_1 Homo sapiens hg19 chr11 108117847 108117848 - GAAAGGAATAGTTGCATGTACAGAGTC 0 GATATCTGCCATCAATTCAATCAAATTTT 0 - ILLUMINA NA 174 TRUE +ATM2 ATM2.chr11.108119823.108119823 ATM2.chr11.108119823.108119823_tile_1 Homo sapiens hg19 chr11 108119823 108119823 - TTGCTAGTAATAGGTTTGGGGGTAGAC 0 GATCAAAATCATTCTGTGACTTCTGAA 0 - ILLUMINA NA 172 TRUE +ATM3 ATM3.chr11.108123551.108123551 ATM3.chr11.108123551.108123551_tile_1 Homo sapiens hg19 chr11 108123551 108123551 - AAGCTATAGCTTAAAATGATAAAGAGCAT 0 ACAAAGAAAAACAAAAAGCTTCACTTAGA 0 - ILLUMINA NA 172 TRUE +ATM4 ATM4.chr11.108137973.108138003 ATM4.chr11.108137973.108138003_tile_1 Homo sapiens hg19 chr11 108137973 108138003 - ACTGCCAAATCAATATAAAGAAGTAAAAGA 0 GATTTCCATTAGTATCATCTTCCATTGAT 0 - ILLUMINA NA 189 TRUE +ATM6 ATM6.chr11.108155132.108155132 ATM6.chr11.108155132.108155132_tile_1 Homo sapiens hg19 chr11 108155132 108155132 - TCGAATAAATAGCCTTAAAACTTAAAGGTT 0 ATCCCACTGTCTCTGGTACCCTCATAG 0 - ILLUMINA NA 179 TRUE +ATM7 ATM7.chr11.108170476.108170479 ATM7.chr11.108170476.108170479_tile_1 Homo sapiens hg19 chr11 108170476 108170479 - ACTCACCAATCTTCTACCAGTGTGTTA 0 ACTTCTCCCAAGCAGCTTCCAACAGCC 0 - ILLUMINA NA 178 TRUE +ATM9 ATM9.chr11.108172421.108172421 ATM9.chr11.108172421.108172421_tile_1 Homo sapiens hg19 chr11 108172421 108172421 - ACAGAACTGTTTTAGATATGCTGGGTA 0 AATGTTTTTCAAACAGGTAACAGCTGC 0 - ILLUMINA NA 182 TRUE +ATM10 ATM10.chr11.108173640.108173640 ATM10.chr11.108173640.108173640_tile_1 Homo sapiens hg19 chr11 108173640 108173640 - CAGGTCATAAACAAGGAATTATATCAGACT 0 ATATCATCCAGGCCTTCAAAAGGG 0 - ILLUMINA NA 191 TRUE +ATM11 ATM11.chr11.108180945.108180945 ATM11.chr11.108180945.108180945_tile_1 Homo sapiens hg19 chr11 108180945 108180945 - CCCTTATTGAGACAATGCCAACATTAA 0 CTAGATAATTTAAATCCAGCCAGAAAGC 0 - ILLUMINA NA 188 TRUE +ATM12 ATM12.chr11.108200958.108200961 ATM12.chr11.108200958.108200961_tile_1 Homo sapiens hg19 chr11 108200958 108200961 - CAAAGTCGGAATACCCACATATCATGT 0 CCTTTACTGTGTATCTTGCATAGAATAAT 0 - ILLUMINA NA 172 TRUE +ATM14 ATM14.chr11.108204681.108204681 ATM14.chr11.108204681.108204681_tile_1 Homo sapiens hg19 chr11 108204681 108204681 - TAGGTTGAAACATATGAAATTTGCCAA 0 GGGACAACAACATCTTCTAAATTCTTAAG 0 - ILLUMINA NA 174 TRUE +ATM15 ATM15.chr11.108205769.108205769 ATM15.chr11.108205769.108205769_tile_1 Homo sapiens hg19 chr11 108205769 108205769 - GACAAAATCCCAAATAAAGCAGAAAGAA 0 CCTGCTAAGCGAAATTCTGCTTTAAATG 0 - ILLUMINA NA 191 TRUE +ATM16 ATM16.chr11.108206594.108206594 ATM16.chr11.108206594.108206594_tile_1 Homo sapiens hg19 chr11 108206594 108206594 - CACCCAACCAAATGGCATCTTTTATAT 0 TTGTCTCAGGTCATCACGGCCCTTCAG 0 - ILLUMINA NA 186 TRUE +ATM17 ATM17.chr11.108218089.108218089 ATM17.chr11.108218089.108218089_tile_1 Homo sapiens hg19 chr11 108218089 108218089 - CTAGGACAACTGTTTATGCTGAAAACA 0 TCTATATGTACAAGTTCTGCTGACTGC 0 - ILLUMINA NA 188 TRUE +ATM18 ATM18.chr11.108225590.108225590 ATM18.chr11.108225590.108225590_tile_1 Homo sapiens hg19 chr11 108225590 108225590 - GCTAAGTGCACAATCTCCTCCTTTCT 0 AACAGAGTTTCCTGAGAGTTTCTCATC 0 - ILLUMINA NA 191 TRUE +ATM19 ATM19.chr11.108236086.108236203 ATM19.chr11.108236086.108236203_tile_1 Homo sapiens hg19 chr11 108236086 108236203 - TGAAGATCACACCCAAGCTTTCCATC 0 TCAGCTACTTTGTTGAAACTCTGGTCA 0 - ILLUMINA NA 185 TRUE +KRAS1 KRAS1.chr12.25378562.25378562 KRAS1.chr12.25378562.25378562_tile_1 Homo sapiens hg19 chr12 25378562 25378562 - TCTTTCCCAGAGAACAAATTAAAAGAGT 0 AGACAAGACAGGTAAGTAACACTGAAA 0 - ILLUMINA NA 187 TRUE +KRAS2 KRAS2.chr12.25380275.25380283 KRAS2.chr12.25380275.25380283_tile_1 Homo sapiens hg19 chr12 25380275 25380283 - TTGTTGTTGAGTTGTATATAACACCTTTT 0 AGTACAGTGCAATGAGGGACCAGTAC 0 - ILLUMINA NA 184 TRUE +KRAS7 KRAS7.chr12.25398255.25398285 KRAS7.chr12.25398255.25398285_tile_1 Homo sapiens hg19 chr12 25398255 25398285 - GGTACTGGTGGAGTATTTGATAGTGTAT 0 GCTAATTCAGAATCATTTTGTGGACGAAT 0 - ILLUMINA NA 191 TRUE +PTPN11_1 PTPN11_1.chr12.112888163.112888211 PTPN11_1.chr12.112888163.112888211_tile_1 Homo sapiens hg19 chr12 112888163 112888211 - TACTGACCTTTCAGAGGTAGGATCTGC 0 GTGTTCTGAATCTTGATGTGGGTGAC 0 - ILLUMINA NA 190 TRUE +PTPN11_10 PTPN11_10.chr12.112926884.112926888 PTPN11_10.chr12.112926884.112926888_tile_1 Homo sapiens hg19 chr12 112926884 112926888 - CAAGAGGCCTAGCAAGAGAATGAGAAT 0 TCTGAGACCGCACCATCTGGATGGTT 0 - ILLUMINA NA 178 TRUE +HNF1A_1 HNF1A_1.chr12.121431413.121431414 HNF1A_1.chr12.121431413.121431414_tile_1 Homo sapiens hg19 chr12 121431413 121431414 - TTGCCGCAGCCCAGACCAAACCAGCA 0 TTGAAACGGTTCCTCCGCCCCTTCTT 0 - ILLUMINA NA 175 TRUE +HNF1A_3 HNF1A_3.chr12.121432070.121432070 HNF1A_3.chr12.121432070.121432070_tile_1 Homo sapiens hg19 chr12 121432070 121432070 - ACATACCACTTACCGTGGACCTTACT 0 CGGTTGGCAAACCAGTTGTAGACA 0 - ILLUMINA NA 181 TRUE +FLT3_1 FLT3_1.chr13.28592620.28592653 FLT3_1.chr13.28592620.28592653_tile_1 Homo sapiens hg19 chr13 28592620 28592653 - CACATCACAGTAAATAACACTCTGGTG 0 TTGTCAGGGGCAATGTGAGGCTGCTATT 0 - ILLUMINA NA 178 TRUE +FLT3_13 FLT3_13.chr13.28602329.28602329 FLT3_13.chr13.28602329.28602329_tile_1 Homo sapiens hg19 chr13 28602329 28602329 - ACTTGAGTTTTACATTTTTAATGCTCCT 0 TGTCAGGTAACCCACTTCCACGAAAA 0 - ILLUMINA NA 171 TRUE +FLT3_14 FLT3_14.chr13.28608244.28608341 FLT3_14.chr13.28608244.28608341_tile_1 Homo sapiens hg19 chr13 28608244 28608341 - CTATCTGCAGAACTGCCTATTCCTAAC 0 TTCCAAGAGAAAATTTAGAGTTTGGTAAG 0 - ILLUMINA NA 190 TRUE +FLT3_22 FLT3_22.chr13.28610138.28610138 FLT3_22.chr13.28610138.28610138_tile_1 Homo sapiens hg19 chr13 28610138 28610138 + CCAGGTCCAAGATGGTAATGGGTAT 0 ATACCAATACTTTGTGAAGCCAAGGTGG 0 + ILLUMINA NA 171 TRUE +RB1_1 RB1_1.chr13.48919244.48919244 RB1_1.chr13.48919244.48919244_tile_1 Homo sapiens hg19 chr13 48919244 48919244 - CCTTTCCAATTTGCTGAAGAGTGCAAA 0 CAGTAACCTTAAAAATTTGTGTTATTTCGT 0 - ILLUMINA NA 182 TRUE +RB1_2 RB1_2.chr13.48923148.48923148 RB1_2.chr13.48923148.48923148_tile_1 Homo sapiens hg19 chr13 48923148 48923148 - GCTAACAGTTAATAAGCCAAGCAGAGA 0 AAATGTGATCCAAGAAACTTTTAGCAC 0 - ILLUMINA NA 178 TRUE +RB1_3 RB1_3.chr13.48942685.48942685 RB1_3.chr13.48942685.48942685_tile_1 Homo sapiens hg19 chr13 48942685 48942685 - ACATAAAGAAACGTGAACAAATCTGAAA 0 GGTGTTCTCTGTGTTTCAAAACTAAATAA 0 - ILLUMINA NA 173 TRUE +RB1_4 RB1_4.chr13.48955538.48955550 RB1_4.chr13.48955538.48955550_tile_1 Homo sapiens hg19 chr13 48955538 48955550 - TTCCCTATATGTTCTTGAGGTAGATGT 0 AATGTTTTATCATTTCTCTTGTCAAGTTG 0 - ILLUMINA NA 182 TRUE +RB1_6 RB1_6.chr13.49027168.49027168 RB1_6.chr13.49027168.49027168_tile_1 Homo sapiens hg19 chr13 49027168 49027168 - TTTGCAGTTTGAATGGTCAACATAACA 0 TAAAGGTGAATCCTATATGAAACATGATG 0 - ILLUMINA NA 178 TRUE +RB1_7 RB1_7.chr13.49033843.49033846 RB1_7.chr13.49033843.49033846_tile_1 Homo sapiens hg19 chr13 49033843 49033846 - GAAGTGCTTGATTTTCTTACTTGGTCC 0 TAGGCTAGCCGATACACTGTGGGAATA 0 - ILLUMINA NA 178 TRUE +RB1_8 RB1_8.chr13.49037877.49037877 RB1_8.chr13.49037877.49037877_tile_1 Homo sapiens hg19 chr13 49037877 49037877 - GGAAAATTACCTACCTCCTGAACAGCA 0 AGTAGTCAGAATTTTATTACATGGTTTTGT 0 - ILLUMINA NA 172 TRUE +RB1_9 RB1_9.chr13.49039164.49039164 RB1_9.chr13.49039164.49039164_tile_1 Homo sapiens hg19 chr13 49039164 49039164 - TGTTTTGGTGGACCCATTACATTAGAT 0 CTTTGATCAAAACACGTTTGAATGTCT 0 - ILLUMINA NA 174 TRUE +AKT1 AKT1.chr14.105246455.105246455 AKT1.chr14.105246455.105246455_tile_1 Homo sapiens hg19 chr14 105246455 105246455 - TCTGACGGGTAGAGTGTGCGTGGCTC 0 GCTCCCCTCAACAACTTCTCTGTG 0 - ILLUMINA NA 173 TRUE +CDH1_1 CDH1_1.chr16.68835649.68835650 CDH1_1.chr16.68835649.68835650_tile_1 Homo sapiens hg19 chr16 68835649 68835650 - GGCGGTGGTGGTGCCCCACTGT 0 CTTTGAATCGGGTGTCGAGGGAAAAA 0 - ILLUMINA NA 171 TRUE +CDH1_2 CDH1_2.chr16.68846137.68846137 CDH1_2.chr16.68846137.68846137_tile_1 Homo sapiens hg19 chr16 68846137 68846137 - ACATTCTCTAGTCTGGAGAGAGTTTTC 0 TTGGTGTCAGTGACTGTGATCACAGCT 0 - ILLUMINA NA 176 TRUE +CDH1_3 CDH1_3.chr16.68847274.68847277 CDH1_3.chr16.68847274.68847277_tile_1 Homo sapiens hg19 chr16 68847274 68847277 - CATCTTGCCAGGTACCATACAAACCTT 0 CACTTTCAGTGTGGTGATTACGACGTT 0 - ILLUMINA NA 178 TRUE +TP53_1 TP53_1.chr17.7574003.7574021 TP53_1.chr17.7574003.7574021_tile_1 Homo sapiens hg19 chr17 7574003 7574021 - ACTAAATGCATGTTGCTTTTGTACCGT 0 AGAGCTGAATGAGGCCTTGGAACTC 0 - ILLUMINA NA 172 TRUE +TP53_3 TP53_3.chr17.7577022.7577129 TP53_3.chr17.7577022.7577129_tile_1 Homo sapiens hg19 chr17 7577022 7577129 - ATCCTGAGTAGTGGTAATCTACTGGGA 0 AGGTAAGCAAGCAGGACAAGAAGCG 0 - ILLUMINA NA 172 TRUE +TP53_17 TP53_17.chr17.7577523.7577574 TP53_17.chr17.7577523.7577574_tile_1 Homo sapiens hg19 chr17 7577523 7577574 - AAAAAGGCCTCCCCTGCTTGCCACAGG 0 ATCATCACACTGGAAGACTCCAGGTCA 0 - ILLUMINA NA 190 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_1 Homo sapiens hg19 chr17 7578190 7578536 - TTTGGATGACAGAAACACTTTTCGACA 0 CCTGCTGCTTATTTGACCTCCCTATAAC 0 - ILLUMINA NA 172 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_2 Homo sapiens hg19 chr17 7578190 7578536 + GACCCCAGTTGCAAACCAGACCTCA 0 TGAGGAATCAGAGGCCTGGGGA 0 + ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_3 Homo sapiens hg19 chr17 7578190 7578536 - TTGTGAGGCGCTGCCCCCACCATGAG 0 GCATCTTATCCGAGTGGAAGGAAATTTG 0 - ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_4 Homo sapiens hg19 chr17 7578190 7578536 + CGTCTCTCCAGCCCCAGCTGCTCACCAT 0 CCACAGCTGCACAGGGCAGGTCTT 0 + ILLUMINA NA 171 TRUE +TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_5 Homo sapiens hg19 chr17 7578190 7578536 - GCATGTTTGTTTCTTTGCTGCCGTCT 0 TTGATTCCACACCCCCGCCCGGC 0 - ILLUMINA NA 179 TRUE +TP53_60 TP53_60.chr17.7579358.7579403 TP53_60.chr17.7579358.7579403_tile_1 Homo sapiens hg19 chr17 7579358 7579403 - AGATGAAGCTCCCAGAATGCCAGAGG 0 TTCTTGCATTCTGGGACAGCCAAGTCT 0 - ILLUMINA NA 185 TRUE +TP53_64 TP53_64.chr17.7579882.7579882 TP53_64.chr17.7579882.7579882_tile_1 Homo sapiens hg19 chr17 7579882 7579882 - ATGGTGTTGGGGGAGGGGGTTCCTTCT 0 CCCCTCTGAGTCAGGAAACATTTTCAG 0 - ILLUMINA NA 182 TRUE +ERBB2_1 ERBB2_1.chr17.37880219.37880261 ERBB2_1.chr17.37880219.37880261_tile_1 Homo sapiens hg19 chr17 37880219 37880261 - CATATCTCCCCAAACCCCAATGAAGAG 0 CTTTGATGGCCACTGGAATTTTCACA 0 - ILLUMINA NA 172 TRUE +ERBB2_4 ERBB2_4.chr17.37880993.37881012 ERBB2_4.chr17.37880993.37881012_tile_1 Homo sapiens hg19 chr17 37880993 37881012 - ATACACCAGTTCAGCAGGTCCTGGGAG 0 TATGCTTCCTGGGGACAAGGGTAC 0 - ILLUMINA NA 190 TRUE +ERBB2_13 ERBB2_13.chr17.37881332.37881440 ERBB2_13.chr17.37881332.37881440_tile_1 Homo sapiens hg19 chr17 37881332 37881440 - TCTGCTCCTTGGTCCTTCACCTAACCT 0 ACATCCTCCAGGTAGCTCATCCCCTGG 0 - ILLUMINA NA 186 TRUE +SMAD4_1 SMAD4_1.chr18.48575169.48575170 SMAD4_1.chr18.48575169.48575170_tile_1 Homo sapiens hg19 chr18 48575169 48575170 - TACAAAAATTGAAACACTATTGAGATCCT 0 CGCATACTGACAATATTTAACATGTTTTAG 0 - ILLUMINA NA 172 TRUE +SMAD4_2 SMAD4_2.chr18.48581198.48581198 SMAD4_2.chr18.48581198.48581198_tile_1 Homo sapiens hg19 chr18 48581198 48581198 - ATGTTGGGAAAGTTGGCAGTGCTGGTA 0 CAAAGTCATGCACATATTCATCCTTCAC 0 - ILLUMINA NA 180 TRUE +SMAD4_3 SMAD4_3.chr18.48584560.48584560 SMAD4_3.chr18.48584560.48584560_tile_1 Homo sapiens hg19 chr18 48584560 48584560 - GCTGTCTAAAAATTAAGGCCCACATGG 0 TGATGCTATCTGCAACAGTCCTTCAC 0 - ILLUMINA NA 188 TRUE +SMAD4_4 SMAD4_4.chr18.48586262.48586262 SMAD4_4.chr18.48586262.48586262_tile_1 Homo sapiens hg19 chr18 48586262 48586262 - ACTCATGTCATGATGAGTATTGTACTC 0 AATGCAAGCTCATTGTGAACAGGCCCT 0 - ILLUMINA NA 184 TRUE +SMAD4_5 SMAD4_5.chr18.48591826.48591919 SMAD4_5.chr18.48591826.48591919_tile_1 Homo sapiens hg19 chr18 48591826 48591919 - CAATACCTTGCTCTCTCAATGGCTTCT 0 AGTAAGCAATGGAACACCAATACTCAG 0 - ILLUMINA NA 188 TRUE +SMAD4_11 SMAD4_11.chr18.48593405.48593405 SMAD4_11.chr18.48593405.48593405_tile_1 Homo sapiens hg19 chr18 48593405 48593405 - GCACTTGGGTAGATCTTATGAACAGCA 0 TGCCTATGTGCAACCTTAGGAAGAAA 0 - ILLUMINA NA 172 TRUE +SMAD4_12 SMAD4_12.chr18.48603032.48603094 SMAD4_12.chr18.48603032.48603094_tile_1 Homo sapiens hg19 chr18 48603032 48603094 - AAAGAATGAAAAGCATACTTACTGATAGC 0 CTGACGCAAATCAAAGACCTTTTAAGAA 0 - ILLUMINA NA 172 TRUE +SMAD4_15 SMAD4_15.chr18.48604668.48604754 SMAD4_15.chr18.48604668.48604754_tile_1 Homo sapiens hg19 chr18 48604668 48604754 - GCATGGTATGAAGTACTTCGTCTAGGA 0 AAGGTCATCAACACCAATTCCAGCAG 0 - ILLUMINA NA 172 TRUE +STK11_1 STK11_1.chr19.1207021.1207092 STK11_1.chr19.1207021.1207092_tile_1 Homo sapiens hg19 chr19 1207021 1207092 - CGCAACTTCTTCTTCTTGAGGATCTTG 0 TAGATGACCTCGGTGGAGTCGATGCGG 0 - ILLUMINA NA 178 TRUE +STK11_4 STK11_4.chr19.1220487.1220502 STK11_4.chr19.1220487.1220502_tile_1 Homo sapiens hg19 chr19 1220487 1220502 - AAAGCCGGGGAGCCCTGGCTGGTC 0 AGATTTTGAGGGTGCCACCGGTGGTG 0 - ILLUMINA NA 181 TRUE +STK11_8 STK11_8.chr19.1221264.1221319 STK11_8.chr19.1221264.1221319_tile_1 Homo sapiens hg19 chr19 1221264 1221319 + TGTACCCCTTCGAAGGGGACAACATCTA 0 GCTTTTGTGCAGAAATGTAGGGTTGG 0 + ILLUMINA NA 177 TRUE +STK11_12 STK11_12.chr19.1223059.1223125 STK11_12.chr19.1223059.1223125_tile_1 Homo sapiens hg19 chr19 1223059 1223125 - ACATCCTGGCCGAGTCAGCAGAGCC 0 ACCGGTCCTTGGTGTCTGGGCTC 0 - ILLUMINA NA 188 TRUE +JAK3_1 JAK3_1.chr19.17945696.17945696 JAK3_1.chr19.17945696.17945696_tile_1 Homo sapiens hg19 chr19 17945696 17945696 - ATCCCTGATCCCACTTTCATTCCCTCA 0 ATGCCCATCAGTGCCCTGGATCCTG 0 - ILLUMINA NA 176 TRUE +JAK3_2 JAK3_2.chr19.17948009.17948009 JAK3_2.chr19.17948009.17948009_tile_1 Homo sapiens hg19 chr19 17948009 17948009 - TAGTGCTGTGTGCACTAATGGCAGACT 0 AGCTTGATGAGCCAAGTGTCGTAC 0 - ILLUMINA NA 190 TRUE +SRC SRC.chr20.36031762.36031762 SRC.chr20.36031762.36031762_tile_1 Homo sapiens hg19 chr20 36031762 36031762 - AAAGAGGAAGGGCCTCGCCCCTGGCAAT 0 TACTGGGGCTCGGTGGACGTGAAGTAG 0 - ILLUMINA NA 191 TRUE +GNAS1 GNAS1.chr20.57484420.57484421 GNAS1.chr20.57484420.57484421_tile_1 Homo sapiens hg19 chr20 57484420 57484421 - ACAGCTGGTTATTCCAGAGGGACTGGG 0 GCGAAGCAGGTCCTGAAACAAAATTGA 0 - ILLUMINA NA 172 TRUE +SMARCB1_1 SMARCB1_1.chr22.24133967.24133990 SMARCB1_1.chr22.24133967.24133990_tile_1 Homo sapiens hg19 chr22 24133967 24133990 - GCGAGTGGTTTTGAAACAGGTTTACA 0 ACATACGGAGGTAGTTTCCCACCTAT 0 - ILLUMINA NA 189 TRUE +SMARCB1_3 SMARCB1_3.chr22.24143240.24143240 SMARCB1_3.chr22.24143240.24143240_tile_1 Homo sapiens hg19 chr22 24143240 24143240 - TTGTGGGGAGCACAAGGTCAAAGCAG 0 ATGCGGTTCCTGTTGATGGTTGTGGA 0 - ILLUMINA NA 175 TRUE +SMARCB1_4 SMARCB1_4.chr22.24145582.24145582 SMARCB1_4.chr22.24145582.24145582_tile_1 Homo sapiens hg19 chr22 24145582 24145582 - ATGTCCTGCGTGTCAGGTCCAGAATCT 0 TTCTGCCCATCGATCTCCATGTCCAG 0 - ILLUMINA NA 176 TRUE +SMARCB1_5_6 SMARCB1_5_6.chr22.24176352.24176357 SMARCB1_5_6.chr22.24176352.24176357_tile_1 Homo sapiens hg19 chr22 24176352 24176357 - ACTCCACCCCCACCCGATCCTCAGGA 0 TGTTGGCAAGACGCCTCATCCGCCTGG 0 - ILLUMINA NA 173 TRUE +GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_1 Homo sapiens hg19 chr19 3114942 3115070 + AGTGCGCGGTCCACCCCCTCCT 0 CTGCCCACCCAGCAGGACGTGCT 0 + ILLUMINA NA 182 TRUE +GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_2 Homo sapiens hg19 chr19 3114942 3115070 - CGGCACACCGGGCAAATGAGCC 0 TAGCCCAAGGTGGCGATGCGGTC 0 - ILLUMINA NA 177 TRUE +GNA11_5 GNA11_5.chr19.3118922.3119051 GNA11_5.chr19.3118922.3119051_tile_1 Homo sapiens hg19 chr19 3118922 3119051 + TCCTGCTCCAGCCGATGTCAGTCT 0 GATCCACTGCTTTGAGAACGTGACAT 0 + ILLUMINA NA 189 TRUE +GNA11_6 GNA11_6.chr19.3119204.3119357 GNA11_6.chr19.3119204.3119357_tile_2 Homo sapiens hg19 chr19 3119204 3119357 + GGATGGAGGAGAGCAAAGCCCTGTT 0 CATGGGGAGGGGCTCGCGGGCA 0 + ILLUMINA NA 189 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_1 Homo sapiens hg19 chr19 3120987 3121177 - AACATCTTCAGGATGAACTCCCGCGCC 0 ACGGCCCACCCAGCTCGACCCCC 0 - ILLUMINA NA 172 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_2 Homo sapiens hg19 chr19 3120987 3121177 + AGGTCCCCAGCGGGACGCCCAG 0 CAGCTCAACCTCAAGGAGTACAACCT 0 + ILLUMINA NA 187 TRUE +GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_3 Homo sapiens hg19 chr19 3120987 3121177 - AAAAATCTCCTCCCGCGGGCAGAG 0 AGGATGGTGTCCTTCACGGCCGC 0 - ILLUMINA NA 185 TRUE +GNAQ_4 GNAQ_4.chr9.80412436.80412564 GNAQ_4.chr9.80412436.80412564_tile_1 Homo sapiens hg19 chr9 80412436 80412564 - CATTCTCATTGTGTCTTCCCTCCTCTA 0 GTAACTGAGTCCATGAAACCTATTTCC 0 - ILLUMINA NA 188 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_1 Homo sapiens hg19 chr9 80409379 80409508 - GCTTAGTGAATATGATCAAGTTCTCGTGG 0 GCTTTCTTGAAATTTGATTTTAGGACTTTT 0 - ILLUMINA NA 174 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_2 Homo sapiens hg19 chr9 80409379 80409508 + AGATAATAAAATGATAATCCATTGCCTGTC 0 TTGGCCCCCTACATCGACCATTCT 0 + ILLUMINA NA 177 TRUE +GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_3 Homo sapiens hg19 chr9 80409379 80409508 - ATTGAATTGACTTGGATGATCATCGTC 0 GGTCAGAGAGAAGAAAATGGATACACT 0 - ILLUMINA NA 182 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_1 Homo sapiens hg19 chr9 80343430 80343583 - GAAAATCATGTATTCCCATCTAGTCGACT 0 TTGCCCTGTGCAGCCTGCGTGTTGA 0 - ILLUMINA NA 172 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_2 Homo sapiens hg19 chr9 80343430 80343583 + TTCACAGCTACTGAGCTGTGGTATGA 0 AGGGGTATGTGATAATTGTTCTAAAGAGAG 0 + ILLUMINA NA 171 TRUE +GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_3 Homo sapiens hg19 chr9 80343430 80343583 - GGTCGTATACAAAAGATGGGTTGGACTTAT 0 GTTCCAGAACTCCTCGGTTATTCTGTT 0 - ILLUMINA NA 187 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_1 Homo sapiens hg19 chr9 80336240 80336429 - ACCATCCTCCAGTTGAACCTGAAGG 0 TTTATTGCCGTCCTGGACTCTGTGTGAGCG 0 - ILLUMINA NA 172 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_2 Homo sapiens hg19 chr9 80336240 80336429 + CAGGGAAGGGCAGGGCGGGTGTCTA 0 ATAATTTTGTCACTGTCTGGGTTCAGG 0 + ILLUMINA NA 172 TRUE +GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_3 Homo sapiens hg19 chr9 80336240 80336429 - CCAATGATGATTGAATACATTAGCAGAT 0 TACTCCCACTTCACGTGCGCCACAGAC 0 - ILLUMINA NA 177 TRUE +[Targets] +TargetA TargetB Target Number Chromosome Start Position End Position Probe Strand Sequence Species Build ID +MPL1_2.chr1.43815008.43815009_tile_1 MPL1_2.chr1.43815008.43815009_tile_1 1 chr1 43814982 43815163 + GGTGGCAGTTTCCTGCACACTACAGGTACCGCCCCCGCCAGGCAGGAGACTGGCGGTGGACCAGGTGGAGCCGAAGGCCTGTAAACAGGCATTCTTGGTTCGCTCTGTGACCCCAGATCTCCGTCCACCGCC Homo sapiens hg19 +NRAS1_7.chr1.115256528.115256531_tile_1 NRAS1_7.chr1.115256528.115256531_tile_1 1 chr1 115256500 115256680 + TCTTGTCCAGCTGTATCCAGTATGTCCAACAAACAGGTTTCACCATCTATAACCACTTGTTTTCTGTAAGAATCCTGGGGGTGTGGAGGGTAAGGGGGCAGGGAGGGAGGGAAGTTCAATTTTTATTA Homo sapiens hg19 +NRAS8_13.chr1.115258730.115258748_tile_1 NRAS8_13.chr1.115258730.115258748_tile_1 1 chr1 115258702 115258884 + TGCGCTTTTCCCAACACCACCTGCTCCAACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGAGCCACATCTACAGTACTTTAAAG Homo sapiens hg19 +ALK1.chr2.29432664.29432664_tile_1 ALK1.chr2.29432664.29432664_tile_1 1 chr2 29432636 29432822 + TCGGGCCATCCCGAAGTCTCCAATCTTGGCCACTCTTCCAGGGCCTGGACAGGTCAAGAGGCAGTTTCTGGCAGCAATGTCTCTGGGAAGAAAGGAAATGCATTTCCTAATTTTATCCCTAGGAAGATGAGTG Homo sapiens hg19 +ALK2.chr2.29443695.29443695_tile_1 ALK2.chr2.29443695.29443695_tile_1 1 chr2 29443667 29443836 + GTTGAATTTGCTGCAGAGCAGAGAGGGATGTAACCAAAATTAACTGAGCTGAGTCTGGGCAAATCTTAAACTGGGAGGAACAGGATACAAAGTTACATTTTCAGCAGCTACAATGTATA Homo sapiens hg19 +IDH1_1_2.chr2.209113112.209113113_tile_1 IDH1_1_2.chr2.209113112.209113113_tile_1 1 chr2 209113084 209113264 + ACGACCTATGATGATAGGTTTTACCCATCCACTCACAAGCCGGGGGATATTTTTGCAGATAATGGCTTCTCTGAAGACCGTGCCACCCAGAATATTTCGTATGGTGCCATTTGGTGATTTCCACATT Homo sapiens hg19 +ERBB4_1_2.chr2.212288942.212288955_tile_1 ERBB4_1_2.chr2.212288942.212288955_tile_1 1 chr2 212288912 212289100 + CCTTTCTCTAATAAATCAGGGATTTCTCGCGTTGGAATTCCATCATAGGGTTTTCCTCCAAAGGTCATCAGTTCCCATATAGTAACTCCTATATTGGAGAAAAAATTCTTACTTAAGCATATTAACAACATATGT Homo sapiens hg19 +ERBB4_3_4.chr2.212530066.212530135_tile_1 ERBB4_3_4.chr2.212530066.212530135_tile_1 1 chr2 212530036 212530210 + TGGATGGCATGGGTGGCACTCCCGATCTGGATCAGCATACTTGAAAATGAAACTGTTTGCCCCCTGTAAGCCATCTGGACATTTTTCCACACAGTTTGGGCCATCTTTAAAATGAGAGCACT Homo sapiens hg19 +ERBB4_5.chr2.212576857.212576857_tile_1 ERBB4_5.chr2.212576857.212576857_tile_1 1 chr2 212576821 212576990 + AATCCACAGTCTGAGCTGACATCAATGATCCTGTGCCAATGCCATCACAAGCTGTAGAAACAAGACTCAGAGTTAGGGGATTGAGAAACTTATTTTTGGCCAATAAATCA Homo sapiens hg19 +ERBB4_6_7.chr2.212578341.212578349_tile_1 ERBB4_6_7.chr2.212578341.212578349_tile_1 1 chr2 212578315 212578499 + CGCACACAAGAACTGGAATCTACCACAAAGTTATCTGATTAAAAAAAAAAAAAAGGTAAAATAAGCATTAATGTTAACATTCAGCAAACAAGCTCAAAACAAGATATTTTAGGGTTTAAAAATGATTAGCA Homo sapiens hg19 +ERBB4_8.chr2.212587147.212587147_tile_1 ERBB4_8.chr2.212587147.212587147_tile_1 1 chr2 212587115 212587285 + CTCCATATGTGTACTTTGCATTGAAATTGTGCTCCAGTTGAAAGGTGGTTGGATTGTAGACAAAGGTTTGGGGACACTGAGTAACACATGCTCCACTGTCATTGAAATTCATGCAGG Homo sapiens hg19 +ERBB4_9.chr2.212589811.212589811_tile_1 ERBB4_9.chr2.212589811.212589811_tile_1 1 chr2 212589783 212589957 + TGTGTCCTTAGGTCCTGAGCAGCCTCCAGCACATTCTCGATGGCAGCAGTCACTGACGTAAGGTCCGTAGCATCTGCCGTCACATTGTTCTGCACACACCGTCCTTGTCACTGCAGAAGAC Homo sapiens hg19 +ERBB4_10.chr2.212652764.212652764_tile_1 ERBB4_10.chr2.212652764.212652764_tile_1 1 chr2 212652706 212652876 + ATAATTCTACTTACATCCTGAACTACCATTTGTTGACACAAGAGTCAAGTTGGAAGGCCATGGGTTCCGAACAATATCTTGCCAATGAATGGTGTCTGCATAACAAAGGAATTT Homo sapiens hg19 +ERBB4_11.chr2.212812157.212812157_tile_1 ERBB4_11.chr2.212812157.212812157_tile_1 1 chr2 212812127 212812311 + TGTCAAGTTCTTTAATCCAAGTTCTTGAAGTCCAAAGTTTCCATCTTTTCTGTAGTTTAAAAATATTGCCAAGGCATATCGATCCTCATAAAGTTTTGTCCCACGAATAATGCGTAAATTCTCCAGAGG Homo sapiens hg19 +VHL1_2.chr3.10183797.10183817_tile_1 VHL1_2.chr3.10183797.10183817_tile_1 1 chr3 10183769 10183952 + GGCTCAACTTCGACGGCGAGCCGCAGCCCTACCCAACGCTGCCGCCTGGCACGGGCCGCCGCATCCACAGCTACCGAGGTACGGGCCCGGCGCTTAGGCCCGACCCAGCAGGGACGATAGCACGGTCTGAAGC Homo sapiens hg19 +VHL3_5.chr3.10188245.10188301_tile_1 VHL3_5.chr3.10188245.10188301_tile_1 1 chr3 10188217 10188401 + GGTTAACCAAACTGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATTTTTGCCAATATCACACTGCCAGGTACTGACGTTTTACTTTTTAAAAAGATAAGGTTGTTGTGGTAAGTACAGGATA Homo sapiens hg19 +VHL6_8.chr3.10191480.10191506_tile_1 VHL6_8.chr3.10191480.10191506_tile_1 1 chr3 10191450 10191634 + TCTGAAAGAGCGATGCCTCCAGGTTGTCCGGAGCCTAGTCAAGCCTGAGAATTACAGGAGACTGGACATCGTCAGGTCGCTCTACGAAGATCTGGAAGACCACCCAAATGTGCAGAAAGACCTGGAGCGG Homo sapiens hg19 +MLH1.chr3.37067240.37067240_tile_1 MLH1.chr3.37067240.37067240_tile_1 1 chr3 37067212 37067394 + GGTTCGTACAGATTCCCGGGAACAGAAGCTTGATGCATTTCTGCAGCCTCTGAGCAAACCCCTGTCCAGTCAGCCCCAGGCCATTGTCACAGAGGATAAGACAGATATTTCTAGTGGCAGGGCTAGGCAG Homo sapiens hg19 +CTNNB1_1_16.chr3.41266040.41266137_tile_1 CTNNB1_1_16.chr3.41266040.41266137_tile_1 1 chr3 41266010 41266180 + ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGC Homo sapiens hg19 +PIK3CA1.chr3.178916876.178916876_tile_1 PIK3CA1.chr3.178916876.178916876_tile_1 1 chr3 178916836 178917024 + TGATGAAACAAGACGACTTTGTGACCTTCGGCTTTTTCAACCCTTTTTAAAAGTAATTGAACCAGTAGGCAACCGTGAAGAAAAGATCCTCAATCGAGAAATTGGTATGATACAATATCCTATTCTAAAATGCAAA Homo sapiens hg19 +PIK3CA2.chr3.178921553.178921553_tile_1 PIK3CA2.chr3.178921553.178921553_tile_1 1 chr3 178921525 178921709 + ATGTAAATATTCGAGACATTGATAAGGTAAAGTCAAATGCTGATGCTTATTATTTTATAGAAATTATTTTAGATAACCTTTTTCTTGCACTATACAGTAATCTGTTGACCTGTAGTATGTTTTCAGATGGT Homo sapiens hg19 +PIK3CA3.chr3.178927980.178927980_tile_1 PIK3CA3.chr3.178927980.178927980_tile_1 1 chr3 178927906 178928082 + TTATAATTTAGACTAGTGAATATTTTTCTTTGTTTTTTAAGGAACACTGTCCATTGGCATGGGGAAATATAAACTTGTTTGATTACACAGACACTCTAGTATCTGGAAAAATGGCTTTGAATC Homo sapiens hg19 +PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 1 chr3 178936044 178936214 + ATCCTCTCTCTGAAATCACTGAGCAGGAGAAAGATTTTCTATGGAGTCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGAATTTGG Homo sapiens hg19 +PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 1 chr3 178938832 178939004 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTCTCAAACAGGAGAAGAAGGATGAAACACAAAAGGTGTGTGACTCTAGTTTGTGTTTGAGACTCTT Homo sapiens hg19 +PIK3CA13_20.chr3.178952007.178952150_tile_1 PIK3CA13_20.chr3.178952007.178952150_tile_1 1 chr3 178951881 178952054 + TATCTAGCTATTCGACAGCATGCCAATCTCTTCATAAATCTTTTCTCAATGATGCTTGGCTCTGGAATGCCAGAACTACAATCTTTTGATGACATTGCATACATTCGAAAGACCCTAGCC Homo sapiens hg19 +PIK3CA13_20.chr3.178952007.178952150_tile_2 PIK3CA13_20.chr3.178952007.178952150_tile_2 1 chr3 178951999 178952184 - TTTCAGTTCAATGCATGCTGTTTAATTGTGTGGAAGATCCAATCCATTTTTGTTGTCCAGCCACCATGATGTGCATCATTCATTTGTTTCATGAAATACTCCAAAGCCTCTTGCTCAGTTTTATCTAAG Homo sapiens hg19 +FGFR3_1_2.chr4.1803564.1803568_tile_1 FGFR3_1_2.chr4.1803564.1803568_tile_1 1 chr4 1803538 1803712 + GCGCTCCCCGCACCGGCCCATCCTGCAGGCGGGGCTGCCGGCCAACCAGACGGCGGTGCTGGGCAGCGACGTGGAGTTCCACTGCAAGGTGTACAGTGACGCACAGCCCCACATCCAGTGGCT Homo sapiens hg19 +FGFR3_3_4.chr4.1806119.1806153_tile_1 FGFR3_3_4.chr4.1806119.1806153_tile_1 1 chr4 1806091 1806277 + CGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTA Homo sapiens hg19 +FGFR3_5_7.chr4.1807862.1807890_tile_1 FGFR3_5_7.chr4.1807862.1807890_tile_1 1 chr4 1807836 1808025 + CCGGGACGTGCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGGGCCGGCTGCCCGTGA Homo sapiens hg19 +FGFR3_8.chr4.1808331.1808331_tile_1 FGFR3_8.chr4.1808331.1808331_tile_1 1 chr4 1808295 1808464 + GCTCCCCGTACCCCGGCATCCCTGTGGAGGAGCTCTTCAAGCTGCTGAAGGAGGGCCACCGCATGGACAAGCCCGCCAACTGCACACACGACCTGTGAGTGGCATCCCTGGCCCTCCACTGGGTCC Homo sapiens hg19 +FGFR3_9.chr4.1808949.1808949_tile_1 FGFR3_9.chr4.1808949.1808949_tile_1 1 chr4 1808921 1809105 + CCTGCTGCCCCCGGCCCCACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAATGTGAGGGGTCCCTAGCAGCCCACCCTGCTGCTGGTGCACAGCCACTCCCCGGCATGAGACTCAGTGC Homo sapiens hg19 +PDGFRA1_4.chr4.55141013.55141049_tile_1 PDGFRA1_4.chr4.55141013.55141049_tile_1 1 chr4 55140981 55141157 + AAACCGAGGTATGAAATTCGCTGGAGGGTCATTGAATCAATCAGCCCAGATGGACATGAATATATTTATGTGGACCCGATGCAGCTGCCTTATGACTCAAGATGGGAGTTTCCAAGAGATGGA Homo sapiens hg19 +PDGFRA5.chr4.55144146.55144146_tile_1 PDGFRA5.chr4.55144146.55144146_tile_1 1 chr4 55144120 55144306 + AACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGG Homo sapiens hg19 +PDGFRA6.chr4.55144547.55144547_tile_1 PDGFRA6.chr4.55144547.55144547_tile_1 1 chr4 55144519 55144703 + CACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATGAAAGCAC Homo sapiens hg19 +PDGFRA7_23.chr4.55152040.55152109_tile_1 PDGFRA7_23.chr4.55152040.55152109_tile_1 1 chr4 55152012 55152184 + CGTCCTCCTGGCACAAGGAAAAATTGTGAAGATCTGTGACTTTGGCCTGGCCAGAGACATCATGCATGATTCGAACTATGTGTCGAAAGGCAGTGTACGTCCTCACTTCCCTCACTGGTCA Homo sapiens hg19 +KIT1.chr4.55561764.55561764_tile_1 KIT1.chr4.55561764.55561764_tile_1 1 chr4 55561736 55561913 + CGACGAGATTAGGCTGTTATGCACTGATCCGGGCTTTGTCAAATGGACTTTTGAGATCCTGGATGAAACGAATGAGAATAAGCAGAATGAATGGATCACGGAAAAGGCAGAAGCCACCAACACCG Homo sapiens hg19 +KIT2.chr4.55592185.55592186_tile_1 KIT2.chr4.55592185.55592186_tile_1 1 chr4 55592155 55592341 + CCTATTTTAACTTTGCATTTAAAGGTAACAACAAAGGTATATTTCTTTTTAATCCAATTTAAGGGGATGTTTAGGCTCTGTCTACCATATCAGTCATGATTTTAAGTTCATTCCAACATTGACCATGTCATTTC Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_1 KIT3_19.chr4.55593464.55593689_tile_1 1 chr4 55593342 55593512 + ATTTCTCTTCCATTGTAGAGCAAATCCATCCCCACACCCTGTTCACTCCTTTGCTGATTGGTTTCGTAATCGTAGCTGGCATGATGTGCATTATTGTGATGATTCTGACCTACAAATA Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_2 KIT3_19.chr4.55593464.55593689_tile_2 1 chr4 55593436 55593609 - TTCTGTGGGGAGAAAGGGAAAAATAGATCACCTTTTAATAATTATTGTCTCAGTCATTAGAGCACTCTGGAGAGAGAACAAATAAATGGTTACCTGTAAATATTTGTAGGTCAGAATCATCA Homo sapiens hg19 +KIT3_19.chr4.55593464.55593689_tile_3 KIT3_19.chr4.55593464.55593689_tile_3 1 chr4 55593556 55593739 + AACCCATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTCAG Homo sapiens hg19 +KIT20_21.chr4.55594221.55594258_tile_1 KIT20_21.chr4.55594221.55594258_tile_1 1 chr4 55594193 55594380 + CAAAGTCCTGAGTTACCTTGGTAATCACATGAATATTGTGAATCTACTTGGAGCCTGCACCATTGGAGGTAAAGCCGTGTCCAAGCTGCCTTTTATTGTCTGTCAGGTTATCAAAACATGACATTTTAATATG Homo sapiens hg19 +KIT22.chr4.55595519.55595519_tile_1 KIT22.chr4.55595519.55595519_tile_1 1 chr4 55595493 55595675 + CAGAATATTGTTGCTATGGTGATCTTTTGAATTTTTTGAGAAGAAAACGTGATTCATTTATTTGTTCAAAGCAGGAAGATCATGCAGAAGCTGCACTTTATAAGAATCTTCTGCATTCAAAGGAGTCT Homo sapiens hg19 +KIT23.chr4.55597495.55597497_tile_1 KIT23.chr4.55597495.55597497_tile_1 1 chr4 55597467 55597652 + CAGCGATAGTACTAATGAGTACATGGACATGAAACCTGGAGTTTCTTATGTTGTCCCAACCAAGGCCGACAAAAGGAGATCTGTGAGAATAGGTGAGTACCTACCTATCAAGCAACCAAGAGTAACTTTAC Homo sapiens hg19 +KIT24_28.chr4.55599320.55599348_tile_1 KIT24_28.chr4.55599320.55599348_tile_1 1 chr4 55599290 55599472 + AGAGACATCAAGAATGATTCTAATTATGTGGTTAAAGGAAACGTGAGTACCCATTCTCTGCTTGACAGTCCTGCAAAGGATTTTTAGTTTCAACTTTCGATAAAAATTGTTTCCTGTGATTTTCATAAT Homo sapiens hg19 +KIT29.chr4.55602694.55602694_tile_1 KIT29.chr4.55602694.55602694_tile_1 1 chr4 55602666 55602850 + CCTGAAAGCATTTTCAACTGTGTATACACGTTTGAAAGTGACGTCTGGTCCTATGGGATTTTTCTTTGGGAGCTGTTCTCTTTAGGTAAAATGATCCTTGCCAAAGACAACTTCATTAGACTCAGAGCATCTT Homo sapiens hg19 +KDR1.chr4.55946114.55946257_tile_1 KDR1.chr4.55946114.55946257_tile_1 1 chr4 55945984 55946155 + CGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCT Homo sapiens hg19 +KDR1.chr4.55946114.55946257_tile_2 KDR1.chr4.55946114.55946257_tile_2 1 chr4 55946098 55946284 - GGATATCACTCCGATGACACAGACACCACCGTGTACTCCAGTGAGGAAGCAGAACTTTTAAAGCTGATAGAGATTGGAGTGCAAACCGGTAGCACAGCCCAGATTCTCCAGCCTGACTCGGGGACCACACTGA Homo sapiens hg19 +KDR3.chr4.55953807.55953807_tile_1 KDR3.chr4.55953807.55953807_tile_1 1 chr4 55953777 55953965 + TTGGGGTCACATACTTCCTCCTCCTCCATACAGGAAACAGGTGAGGTAGGCAGAGAGAGTCCAGAATCCTCTTCCATGCTCAAAGTCTCTGATATCGGAAGAACAATGTAGTCTTTGCCATCCTGAAACAATAAA Homo sapiens hg19 +KDR4.chr4.55955111.55955127_tile_1 KDR4.chr4.55955111.55955127_tile_1 1 chr4 55955085 55955257 + CCCCGTGCCAGCAGTCCAGCATGGTCTGGTACCTAGAGAAGCAAAACACTGATTTCATTAAATGCCTCTTTCTTCCTGAATGCTGAAAATAAGCACTTAAATGAGTACACATTTGTAAAGAG Homo sapiens hg19 +KDR6.chr4.55960989.55961023_tile_1 KDR6.chr4.55960989.55961023_tile_1 1 chr4 55960959 55961129 + TCACTGAGGGACTTCTCCTCCACAAATCCAGAGCTGGCTGAGCTCTGGCTACTGGTGATGCTGTCCAAGCGCCGTTTCAGATCCACAGGGATTGCTCCAACGTAGTCTTTCCCTTGA Homo sapiens hg19 +KDR8.chr4.55962507.55962507_tile_1 KDR8.chr4.55962507.55962507_tile_1 1 chr4 55962477 55962653 + GCTCCTTCTACAAATACAGTACAAAGAGGGAAATCATAGGTATGGACATTTCCTTCAATAATTGGGGTCCCTCCCTCCCTGCATGCCACTATACAACTTACCCTCCGGGGTAACACAGCTGTGA Homo sapiens hg19 +KDR9.chr4.55972964.55972964_tile_1 KDR9.chr4.55972964.55972964_tile_1 1 chr4 55972936 55973106 + ACTGAGACAGCTTGGCTATAAGAAAGAGATAACAGCGCATATTATGATTTAATTTTTCTTTAATTAGAGTCAAGAGTAAGGAAAAGATTCAGACTTTGGTTATTCTGTTCTTAGAAA Homo sapiens hg19 +KDR10.chr4.55979623.55979623_tile_1 KDR10.chr4.55979623.55979623_tile_1 1 chr4 55979595 55979775 + CTCGGTTTACAAGTTTCTTATGCTGATGCTGAAAAAAAGAGTTGACTGAACTTCCAAAGCACAGCATATAACATTACCCAATAACTTCTAGTAACACACAGAATTAAATCTGGGCTTTGGTAAACATT Homo sapiens hg19 +KDR11.chr4.55980348.55980348_tile_1 KDR11.chr4.55980348.55980348_tile_1 1 chr4 55980320 55980496 + TGCTGTACAATTTAAGACAAGCTTTTCTCCAACAGATAGTTCAATTCCATGAGACGGACTCAGAACCACATCATAAATCCTATACCCTAGAGCAAGTAAATTGAAAAAACAGAACATGAGAGA Homo sapiens hg19 +FBXW7_1.chr4.153245446.153245446_tile_1 FBXW7_1.chr4.153245446.153245446_tile_1 1 chr4 153245416 153245604 + AACGACTGGTGCCCTGTTAACGTGTGAATGCAATTCCCTGTCTCCACATCCCAAACACGGATTGATGTATCAAGAGATCCACTCACCACATGGATACCATCAAACTACAAAAGACACAGTTTATTAGAATAGA Homo sapiens hg19 +FBXW7_2.chr4.153247288.153247366_tile_1 FBXW7_2.chr4.153247288.153247366_tile_1 1 chr4 153247248 153247417 + TTGAACACAGCGGACTGCTGCAACATGACCCATCAAAACATGTAAACACTGGCCTGTCTCAATATCCCAAACCCTAAGAGTGGCATCTCGAGAACCGCTAACAACTCTGCAG Homo sapiens hg19 +FBXW7_5.chr4.153249384.153249384_tile_1 FBXW7_5.chr4.153249384.153249384_tile_1 1 chr4 153249338 153249520 + TTCATGAAGATGCATACAACGCACAGTGGAAGTATGCCCATATAAGGTGTGTATACATTCTCCAGTCTCTGCATTCCACACTTTGAGTGTCCGATCTGTAGATCCACTAATGATGATGTTGTCTCTCAT Homo sapiens hg19 +FBXW7_7.chr4.153250883.153250883_tile_1 FBXW7_7.chr4.153250883.153250883_tile_1 1 chr4 153250853 153251031 + ATTCGGTTACCACAAAACTGTAAGCATGTGATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGA Homo sapiens hg19 +FBXW7_8.chr4.153258983.153258983_tile_1 FBXW7_8.chr4.153258983.153258983_tile_1 1 chr4 153258953 153259142 + TCGTTGAAACTGGGGTTCTATCACTTGCATCATATGTTTTACTTGTGTTGGTTCACAACTATCAATGAGTTCATCTAAAGCAAGCAATTTCTCTGGTCCACTCCAGCTCTATCAAAGAGAATTAGAAATTTT Homo sapiens hg19 +APC1.chr5.112173917.112173917_tile_1 APC1.chr5.112173917.112173917_tile_1 1 chr5 112173887 112174071 + AAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGA Homo sapiens hg19 +APC2.chr5.112174631.112174631_tile_1 APC2.chr5.112174631.112174631_tile_1 1 chr5 112174603 112174775 + TCGAGTGGGTTCTAATCATGGAATTAATCAAAATGTAAGCCAGTCTTTGTGTCAAGAAGATGACTATGAAGATGATAAGCCTACCAATTATAGTGAACGTTACTCTGAAGAAGAACAGC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_1 APC3_42.chr5.112175162.112175958_tile_1 1 chr5 112175034 112175208 - TCTGCTTCCTGTGTCGTCTGATTACATCCTATTTCATCTTCAGCTGATGACAAAGATGATAATGAACTACATCTTGAAAAACATATTGGAGTATCTTCTACACAATAAGTCTGTATTGTT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_2 APC3_42.chr5.112175162.112175958_tile_2 1 chr5 112175128 112175297 + ATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCAC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_3 APC3_42.chr5.112175162.112175958_tile_3 1 chr5 112175216 112175386 - CCTGAAGAAAATTCAACAGCTTTGTGCCTGGCTGATTCTGAAGATAAACTAGAACCCTGCAGTCTGCTGGATTTGGTTCTAGGGTGCTGTGACACTGCTGGAACTTCGCTCACAGGAT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_4 APC3_42.chr5.112175162.112175958_tile_4 1 chr5 112175306 112175475 + CACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_5 APC3_42.chr5.112175162.112175958_tile_5 1 chr5 112175394 112175566 - GCCACTTACCATTCCACTGCATGGTTCACTCTGAACGGAGCTGGCAATCGAACGACTCTCAAAACTATCAAGTGAACTGACAGAAGTACATCTGCTAAACATGAGTGGGGTCTCCTGAAC Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_6 APC3_42.chr5.112175162.112175958_tile_6 1 chr5 112175512 112175683 + GCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_7 APC3_42.chr5.112175162.112175958_tile_7 1 chr5 112175630 112175799 - CCGTGGCAAAATGTAATAAAGTATCAGCATCTGGAAGAACCTGGACCCTCTGAACTGCAGCATTTACTGCAGCTTGCTTAGGTCCACTCTCTCTCTTTTCAGCAGTAGGTGCTTT Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_8 APC3_42.chr5.112175162.112175958_tile_8 1 chr5 112175740 112175911 + GGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAA Homo sapiens hg19 +APC3_42.chr5.112175162.112175958_tile_9 APC3_42.chr5.112175162.112175958_tile_9 1 chr5 112175854 112176042 - AGTATTTCAATATCATCATCATCTGAATCATCTAATAGGTCCTTTTCAGAATCAATAGTTTTTTCTGCCTCTTTCTCTTGGTTTTCATTTGATTCTTTAGGCTGCTCTGATTCTGTTTCATTCCCATTGTCATTT Homo sapiens hg19 +CSF1R1_3.chr5.149433644.149433646_tile_1 CSF1R1_3.chr5.149433644.149433646_tile_1 1 chr5 149433616 149433799 + GATAGTTGTTGGGCTGCAGCAAGGGCTGGGCGATATCCCCTTGCTCGCAGCAGGTCAGGTGCTCACTAGAGCTCTCCTCCTCCAGCTCACTGCTGCTGCTGCCGCTGCCACCGCTTCTGCTGCTGCTCGGC Homo sapiens hg19 +CSF1R4.chr5.149453044.149453044_tile_1 CSF1R4.chr5.149453044.149453044_tile_1 1 chr5 149453016 149453189 + CAAGTAGGCACTCTCTGGAAAGCAGAACACACAAGCATCTGGCATTAGTGGGAAGATGTCCTTGTTTATTTGTCCATTTTGTCATCCACCCATTGATCCAGTCCCTGAGCAGCTATGTCAC Homo sapiens hg19 +NPM1.chr5.170837547.170837548_tile_1 NPM1.chr5.170837547.170837548_tile_1 1 chr5 170837493 170837677 + TTTTTTTTCCAGGCTATTCAAGATCTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAGTTTAAACAATTTGTTAAAAAATTTTCCGTCTTATTTCATTTCTGTAACAGTTGATATCTGGCTGTCCTTTTTA Homo sapiens hg19 +EGFR1.chr7.55211080.55211080_tile_1 EGFR1.chr7.55211080.55211080_tile_1 1 chr7 55211052 55211238 + AGAGGAAATATGTACTACGAAAATTCCTATGCCTTAGCAGTCTTATCTAACTATGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTACAGGGTGAGAGGCTGGGATGCCAAGGCTGGGGGT Homo sapiens hg19 +EGFR2.chr7.55221822.55221822_tile_1 EGFR2.chr7.55221822.55221822_tile_1 1 chr7 55221792 55221964 + GGTGCCACCTGCGTGAAGAAGTGTCCCCGTGAGTCCTCCTCTGTGGGCCCTCTAACTGGTCAGGCATCCTTGTCCCGCTCTGTCTCCTGCTGAGCCCTGGAGTATCCCATCTTGGAGAGT Homo sapiens hg19 +EGFR3.chr7.55233043.55233043_tile_1 EGFR3.chr7.55233043.55233043_tile_1 1 chr7 55233019 55233203 + GGAGTCATGGGAGAAAACAACACCCTGGTCTGGAAGTACGCAGACGCCGGCCATGTGTGCCACCTGTGCCATCCAAACTGCACCTACGGGTGAGTGGAAAGTGAAGGAGAACAGAACATTTCCTCTCTTGCAAAT Homo sapiens hg19 +EGFR4.chr7.55241677.55241708_tile_1 EGFR4.chr7.55241677.55241708_tile_1 1 chr7 55241649 55241827 + AGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAGGTAAGGTCCCTGGCACAGGCCTCTGGGCTGGGCCGCAGGGCCTCTCATGGTCTGGTGGGGAGCC Homo sapiens hg19 +EGFR9.chr7.55242418.55242511_tile_1 EGFR9.chr7.55242418.55242511_tile_1 1 chr7 55242388 55242576 + GACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCT Homo sapiens hg19 +EGFR44.chr7.55249005.55249131_tile_1 EGFR44.chr7.55249005.55249131_tile_1 1 chr7 55248879 55249052 + TCTTCACCTGGAAGGGGTCCATGTGCCCCTCCTTCTGGCCACCATGCGAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTG Homo sapiens hg19 +EGFR44.chr7.55249005.55249131_tile_2 EGFR44.chr7.55249005.55249131_tile_2 1 chr7 55249003 55249178 - CAGTTGAGCAGGTACTGGGAGCCAATATTGTCTTTGTGTTCCCGGACATAGTCCAGGAGGCAGCCGAAGGGCATGAGCTGCGTGATGAGCTGCACGGTGGAGGTGAGGCAGATGCCCAGCAGGCGGC Homo sapiens hg19 +EGFR54.chr7.55259514.55259524_tile_1 EGFR54.chr7.55259514.55259524_tile_1 1 chr7 55259486 55259662 + GCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTAAGGAGGTGGCTTTAGGTCAGCCAGCATTTTCCTGACACCAGGGACCAGGCTGCCTTCCCACTAGC Homo sapiens hg19 +MET1.chr7.116339642.116339642_tile_1 MET1.chr7.116339642.116339642_tile_1 1 chr7 116339614 116339792 + AGCCCAGCCAGTGTCCTGACTGTGTGGTGAGCGCCCTGGGAGCCAAAGTCCTTTCATCTGTAAAGGACCGGTTCATCAACTTCTTTGTAGGCAATACCATAAATTCTTCTTATTTCCCAGATCAT Homo sapiens hg19 +MET2.chr7.116340262.116340262_tile_1 MET2.chr7.116340262.116340262_tile_1 1 chr7 116340234 116340420 + AACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGAGCACTGCTTTAATAGGGTAAGTCACATCAGTTCCCCACTTATAAACTGTGAGGTATAAATTAGAAATAAGT Homo sapiens hg19 +MET3.chr7.116411990.116411990_tile_1 MET3.chr7.116411990.116411990_tile_1 1 chr7 116411958 116412127 + GCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATATACCTCAGTGGGTTGT Homo sapiens hg19 +MET4.chr7.116417463.116417464_tile_1 MET4.chr7.116417463.116417464_tile_1 1 chr7 116417431 116417620 + TATATCATGGGACTTTGTTGGACAATGATGGCAAGAAAATTCACTGTGCTGTGAAATCCTTGAACAGTAAGTGGCATTTTATTTAACCATGGAGTATACTTTTGTGGTTTGCAACCTAATAAATAGCTTATAATA Homo sapiens hg19 +MET6.chr7.116423413.116423474_tile_1 MET6.chr7.116423413.116423474_tile_1 1 chr7 116423385 116423555 + TGTATGATAAAGAATACTATAGTGTACACAACAAAACAGGTGCAAAGCTGCCAGTGAAGTGGATGGCTTTGGAAAGTCTGCAAACTCAAAAGTTTACCACCAAGTCAGATGTGGTAAT Homo sapiens hg19 +SMO1.chr7.128845101.128845101_tile_1 SMO1.chr7.128845101.128845101_tile_1 1 chr7 128845073 128845257 + GGTTCGGACAGACAACCCCAAGAGCTGGTACGAGGACGTGGAGGGCTGCGGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCACCAGGACATGCACAGCTACATCGCGGCCTTCGGGGCCGTCACGGGC Homo sapiens hg19 +SMO2.chr7.128846040.128846040_tile_1 SMO2.chr7.128846040.128846040_tile_1 1 chr7 128846010 128846194 + TACGCCCTGATGGCTGGTGTGGTTTGGTTTGTGGTCCTCACCTATGCCTGGCACACTTCCTTCAAAGCCCTGGGCACCACCTACCAGCCTCTCTCGGGCAAGACCTCCTACTTCCACCTGCTCACCTGGTC Homo sapiens hg19 +SMO3.chr7.128846374.128846374_tile_1 SMO3.chr7.128846374.128846374_tile_1 1 chr7 128846348 128846536 + CGTGCTGGCCCCAATCGGCCTGGTGCTCATCGTGGGAGGCTACTTCCTCATCCGAGGTGAGTGAAGACCAGGCCAGGACCAGTTGGGCAACAAAATATACTGGGCACTTGCTGCCAGTACTGGGAGCTGCCAGCACG Homo sapiens hg19 +SMO4.chr7.128850341.128850341_tile_1 SMO4.chr7.128850341.128850341_tile_1 1 chr7 128850311 128850499 + GCACCTGGGTCTGGACCAAGGCCACGCTGCTCATCTGGAGGCGTACCTGGTGCAGGTGGGCATGGCAGCCAGCCCCTCCTGCCCTGCCCGCCTCACCCTCAGCCTTGGGACCCCATCTTTAGGTTTTGTCGGGTCCTG Homo sapiens hg19 +SMO5.chr7.128851593.128851593_tile_1 SMO5.chr7.128851593.128851593_tile_1 1 chr7 128851563 128851734 + GTCACCCCTGTGGCAACTCCAGGTATGAGAGTTCAAGCTTCTGGAGGAAGGTGGGGGGAGCACAGAGGCTGGGGGCTTCTGGGACTGGAGTACAGGGGCTGTCGGAGGAGGAGGAAGAG Homo sapiens hg19 +BRAF1.chr7.140453121.140453193_tile_1 BRAF1.chr7.140453121.140453193_tile_1 1 chr7 140453093 140453267 + CACTCCATCGAGATTTCACTGTAGCTAGACCAAAATCACCTATTTTTACTGTGAGGTCTTCATGAAGAAATATATCTGAGGTGTAGTAAGTAAAGGAAAACAGTAGATCTCATTTTCCTATC Homo sapiens hg19 +BRAF28.chr7.140481397.140481478_tile_1 BRAF28.chr7.140481397.140481478_tile_1 1 chr7 140481369 140481545 + ACTGTTCCAAATGATCCAGATCCAATTCTTTGTCCCACTGTAATCTGCCCATCAGGAATCTCCCAATCATCACTCGAGTCCCGTCTACCAAGTGTTTTCTTGATAAAAACAGTAAAAAAGTCA Homo sapiens hg19 +FGFR1_1.chr8.38282209.38282209_tile_1 FGFR1_1.chr8.38282209.38282209_tile_1 1 chr8 38282183 38282360 + GGGGACCGCTCTGTGGAAGATGGGAGAGGAGGCACTTGTCATGGGGACCTTGCCATGGCTAAAGAGGGGTGGGCTCACCTGCGCCCCACTTGGCTTTCCCAGTGATGGGTTGTAAACCTCCCAGCAC Homo sapiens hg19 +FGFR1_2.chr8.38285938.38285938_tile_1 FGFR1_2.chr8.38285938.38285938_tile_1 1 chr8 38285908 38286090 + TCCGAGGAGGGGAGAGCATCTATGGGAAGAAGAAGGGGCACTGAGGTTCCTCCTAGGGACCCCTAGATTTCACCAAGGCTAGTGCAGTTCCAGATGAACACGGACACCCTCCCCATGGGGATCCCAGTC Homo sapiens hg19 +JAK2_1.chr9.5073769.5073770_tile_1 JAK2_1.chr9.5073769.5073770_tile_1 1 chr9 5073737 5073923 + TATGTGTCTGTGGAGACGAGAGTAAGTAAAACTACAGGCTTTCTAATGCCTTTCTCAGAGCATCTGTTTTTGTTTATATAGAAAATTCAGTTTCAGGATCACAGCTAGGTGTCAGTGTAAACTATAATTT Homo sapiens hg19 +CDKN2A1.chr9.21971153.21971187_tile_1 CDKN2A1.chr9.21971153.21971187_tile_1 1 chr9 21971123 21971308 + GGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCC Homo sapiens hg19 +ABL1_1.chr9.133738330.133738364_tile_1 ABL1_1.chr9.133738330.133738364_tile_1 1 chr9 133738302 133738491 + CCATGAAGCACAAGCTGGGCGGGGGCCAGTACGGGGAGGTGTACGAGGGCGTGTGGAAGAAATACAGCCTGACGGTGGCCGTGAAGACCTTGAAGGTAGGCTGGGACTGCCGGGGGTGCCCAGGGTACGTGGGGCAAG Homo sapiens hg19 +ABL1_9.chr9.133747520.133747520_tile_1 ABL1_9.chr9.133747520.133747520_tile_1 1 chr9 133747476 133747664 + TTTCCTTCTGCAGGAGGACACCATGGAGGTGGAAGAGTTCTTGAAAGAAGCTGCAGTCATGAAAGAGATCAAACACCCTAACCTGGTGCAGCTCCTTGGTGAGTAAGCCCGGGGCTCTGAAGAGAGGGTCTCGCGCCGC Homo sapiens hg19 +ABL1_10.chr9.133748283.133748414_tile_1 ABL1_10.chr9.133748283.133748414_tile_1 1 chr9 133748157 133748327 - CCCGTAGGTCATGAACTCAGTGATGATATAGAACGGGGGCTCCCGGGTGCAGACCCCTGCCAACAAGACAACGAGGACTTCAACACGTGGCTCCGCTCCCAACTGAACAAACAACT Homo sapiens hg19 +ABL1_10.chr9.133748283.133748414_tile_2 ABL1_10.chr9.133748283.133748414_tile_2 1 chr9 133748277 133748457 + GAACCTCCTGGACTACCTGAGGGAGTGCAACCGGCAGGAGGTGAACGCCGTGGTGCTGCTGTACATGGCCACTCAGATCTCGTCAGCCATGGAGTACCTGGAGAAGAAAAACTTCATCCACAGGTAGGGGCCT Homo sapiens hg19 +ABL1_16.chr9.133750356.133750356_tile_1 ABL1_16.chr9.133750356.133750356_tile_1 1 chr9 133750328 133750516 + GCCCATGCTGGAGCCAAGTTCCCCATCAAATGGACTGCACCCGAGAGCCTGGCCTACAACAAGTTCTCCATCAAGTCCGACGTCTGGGGTAAGGGCTGCTGCTGCACTGAAGTGGTCCTTCCTGACTACAGGAGGGTT Homo sapiens hg19 +NOTCH1_1.chr9.139397768.139397768_tile_1 NOTCH1_1.chr9.139397768.139397768_tile_1 1 chr9 139397740 139397928 + CCAGGTAGACGATGGAGCTGGGCGGACAATCAGAGAGGGGCTGGGACCCGAGGCTTCCTCCTCCCCCGCCCACCGGCCAGGGATGCTGCCGCAGGACACTGAGGCCCATGACGCCACAGTCAGGACATGGTGAGGC Homo sapiens hg19 +NOTCH1_2.chr9.139399344.139399422_tile_1 NOTCH1_2.chr9.139399344.139399422_tile_1 1 chr9 139399316 139399485 + GCAGCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGCGCAGCTGCTCCGGCGGCATCAGCACCACCACCACCAGCGTGCCGGCCGCCAGCCTCTCGGGTACATGCTCCGC Homo sapiens hg19 +RET1.chr10.43609078.43609104_tile_1 RET1.chr10.43609078.43609104_tile_1 1 chr10 43609048 43609226 + CTGCTTCCCTGAGGAGGAGAAGTGCTTCTGCGAGCCCGAAGACATCCAGGGTGAGTGGGTGGCGGCCGGGACCACCACCACCTCCCAGCCCCACAGAGGTCTCAACAGCACATCTGAGGTCCCAACAA Homo sapiens hg19 +RET2_9.chr10.43609940.43609950_tile_1 RET2_9.chr10.43609940.43609950_tile_1 1 chr10 43609902 43610075 - TGGCTTGTGGGCAAACTTGTGGTAGCAGTGGATGCAGAAGGCAGACAGCAGCACCGAGACGATGAAGGAGAAGAGGACAGCGGCTGCGATCACCGTGCGGCACAGCTCGTCGCACAGTGG Homo sapiens hg19 +RET10.chr10.43613840.43613840_tile_1 RET10.chr10.43613840.43613840_tile_1 1 chr10 43613810 43613998 + CGAGTGAGCTGCGAGACCTGCTGTCAGAGTTCAACGTCCTGAAGCAGGTCAACCACCCACATGTCATCAAATTGTATGGGGCCTGCAGCCAGGATGGTAAGGCCAGCTGCAGGGTGAGGTGGGCAGCCACTGCACCCAG Homo sapiens hg19 +RET11_12.chr10.43615567.43615569_tile_1 RET11_12.chr10.43615567.43615569_tile_1 1 chr10 43615533 43615703 + CCTGGTAGCTGAGGGGCGGAAGATGAAGATTTCGGATTTCGGCTTGTCCCGAGATGTTTATGAAGAGGATTCCTACGTGAAGAGGAGCCAGGTGCCCAGTCCCGGGGATGAGGCGGGG Homo sapiens hg19 +RET13.chr10.43617416.43617416_tile_1 RET13.chr10.43617416.43617416_tile_1 1 chr10 43617388 43617564 + ATGGCAATTGAATCCCTTTTTGATCATATCTACACCACGCAAAGTGATGTGTAAGTGTGGGTGTTGCTCTCTTGGGGTGGAGGTTACAGAAACACCCTTATACATGTAGTGGGGCCACGACGC Homo sapiens hg19 +PTEN1.chr10.89624242.89624244_tile_1 PTEN1.chr10.89624242.89624244_tile_1 1 chr10 89624214 89624388 + CAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACCTTTCTGTCACTCTCTTAGAACGTGG Homo sapiens hg19 +PTEN3.chr10.89685307.89685307_tile_1 PTEN3.chr10.89685307.89685307_tile_1 1 chr10 89685275 89685459 + ATATACAATCTGTAAGTATGTTTTCTTATTTGTATGCTTGCAAATATCTTCTAAAACAACTATTAAGTGAAAGTTATCTGCTTGTTAGAGTGAGGTAGAGTTAAAGATACATTTTAACAGAATTGTATT Homo sapiens hg19 +PTEN4.chr10.89711893.89711900_tile_1 PTEN4.chr10.89711893.89711900_tile_1 1 chr10 89711865 89712039 + GTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN7.chr10.89717615.89717772_tile_1 1 chr10 89717489 89717668 + ATATTGCTGATATTAATCATTAAAATCGTTTTTGACAGTTTGACAGTTAAAGGCATTTCCTGTGAAATAATACTGGTATGTATTTAACCATGCAGATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_2 PTEN7.chr10.89717615.89717772_tile_2 1 chr10 89717615 89717801 - TTTAGCATCTTGTTCTGTTTGTGGAAGAACTCTACTTTGATATCACCACACACAGGTAACGGCTGAGGGAACTCAAAGTACATGAACTTGTCTTCCCGTCGTGTGGGTCCTGAATTGGAGGAATATATCTTCACC Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 1 chr10 89720684 89720870 + CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_2 PTEN13.chr10.89720716.89720852_tile_2 1 chr10 89720814 89720991 - TTCTTCATCAGCTGTACTCCTAGAATTAAACACACATCACATACATACAAGTCAACAACCCCCACAAAATGTTTAATTTAACTGACCTTAAAATTTGGAGAAAAGTATCGGTTGGCTTT Homo sapiens hg19 +FGFR2_1.chr10.123258034.123258034_tile_1 FGFR2_1.chr10.123258034.123258034_tile_1 1 chr10 123258006 123258184 + GATTTATGATATTCTTGTGTTTCCCAATCATCTTCATCATCTCCATCTCTGACACCAGATCAGAAAGGTCTTTCTCTGTGGCATCATCTATGAACAGTAGGCATATTCACAAATCAGTTCATTTC Homo sapiens hg19 +FGFR2_2.chr10.123274774.123274803_tile_1 FGFR2_2.chr10.123274774.123274803_tile_1 1 chr10 123274746 123274930 + CAGTAAATGGCTATCTCCAGGTAGTCTGGGGAAGCTGTAATCTCCTTTTCTCTTCCAGGCGCTAGATTGCAGATCACAGGAGGAGGAACAGATAAGCAGGCCATAGAGTTAGCACACCAGACTGACGCATC Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_1 FGFR2_5.chr10.123279503.123279677_tile_1 1 chr10 123279385 123279555 + AACAGGAAATCAAAGAACCTGTGGCCAAACCCATGAAGGAGACCCCAGTTGTGGGTACCTTTAGATTCAGAAAGTCCTCACCTTGAGAACCTTGAGGTAGGGCAGCCCGTCGGGCCC Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_2 FGFR2_5.chr10.123279503.123279677_tile_2 1 chr10 123279471 123279640 - ACGTAGAGTTTGTCTGCAAGGTTTACAGTGATGCCCAGCCCCACATCCAGTGGATCAAGCACGTGGAAAAGAACGGCAGTAAATACGGGCCCGACGGGCTGCCCTACCTCAAGGTT Homo sapiens hg19 +FGFR2_5.chr10.123279503.123279677_tile_3 FGFR2_5.chr10.123279503.123279677_tile_3 1 chr10 123279587 123279769 + TCTCCTCCGACCACTGTGGAGGCATTTGCCGGCAGTCCGGCTTGGAGGATGGGCCGGTGAGGCGATCGCTCTGGTGGAGAGAGGGAAGAAAGGAGGAGTGGGGATGGGAGAATGAGAGACCAATAAATA Homo sapiens hg19 +HRAS1.chr11.533873.533875_tile_1 HRAS1.chr11.533873.533875_tile_1 1 chr11 533843 534021 + CCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAATCCTGCAGGAGGACAGGGCTCAGGGACCCCCTCAGGACCTTCCGTGGGGGGA Homo sapiens hg19 +HRAS6.chr11.534285.534289_tile_1 HRAS6.chr11.534285.534289_tile_1 1 chr11 534251 534434 + GCCCACACCGCCGGCGCCCACCACCACCAGCTTATATTCCGTCATCGCTCCTCAGGGGCCTGCGGCCCGGGGTCCTCCTACAGGGTCTCCTGCCCCACCTGCCAAGGAGGGCCCTGCTCAGCCAGGCCCAGGC Homo sapiens hg19 +ATM1.chr11.108117847.108117848_tile_1 ATM1.chr11.108117847.108117848_tile_1 1 chr11 108117817 108117989 + TGTCACCAGGTACAGTAAGTAGGTCATGTCACATTTAGAAATTTCCTGTTAATTTTTTTTTTAAACTGGGCATTTTGGGCTTTTAAAACCTGTGTTCTCACAAAAAGCCTATAAAAT Homo sapiens hg19 +ATM2.chr11.108119823.108119823_tile_1 ATM2.chr11.108119823.108119823_tile_1 1 chr11 108119793 108119963 + TTGTGCCTTGGTAAAGTGTTACCATTTTCTCATTCAGTGTCATTTTAATCTCTTGTATGTTATTTTTCAGAAAACTTTCAGTGGAATCCTTTCATCTCAACCAGAACTAAGTCATTT Homo sapiens hg19 +ATM3.chr11.108123551.108123551_tile_1 ATM3.chr11.108123551.108123551_tile_1 1 chr11 108123513 108123683 + AGTAATTTTCCTCATCTTGTACTGGAGAAAATTCTTGTGAGTCTCACTATGAAAAACTGTAAAGCTGCAATGAATTTTTTCCAAAGCGTGCCAGAATGGTATGTTATCTAATA Homo sapiens hg19 +ATM4.chr11.108137973.108138003_tile_1 ATM4.chr11.108137973.108138003_tile_1 1 chr11 108137939 108138126 + TAATGGAGGTGGAGGATCAGTCATCCATGAATCTATTTAACGATTACCCTGATAGTAGTGTTAGTGATGCAAACGAACCTGGAGAGAGCCAAAGTACCATAGGTAAATACATATTTACTACTTGGGATT Homo sapiens hg19 +ATM6.chr11.108155132.108155132_tile_1 ATM6.chr11.108155132.108155132_tile_1 1 chr11 108155104 108155281 + GGCACAGCAAAGAGAGACTGCTACCAAGGTCTATGATATGCTTAAAAGTGAAAACTTATTGGGAAAACAGGTATGGCTTCAATTTTTATGTACTTTTCATTCCCTGAATGATATGAGATAT Homo sapiens hg19 +ATM7.chr11.108170476.108170479_tile_1 ATM7.chr11.108170476.108170479_tile_1 1 chr11 108170442 108170618 + GGGTCCTATAGATTTCTCTACCATAGCTATACAACATAGTAAAGATGCATCTTATACCAAGGCCCTTAAGTTATTTGAAGATAAAGAACTTCAGTGGACCTTCATAATGCTGACCTACCTGAA Homo sapiens hg19 +ATM9.chr11.108172421.108172421_tile_1 ATM9.chr11.108172421.108172421_tile_1 1 chr11 108172391 108172571 + TTAGCCACAAAGACTGGACATAGTTTCTGGGAGATTTATAAGATGACAACAGATCCAATGCTGGCCTATCTACAGCCTTTTAGAACATCAAGAAAAAAGGTCTCTTAAGTAATAAATGTTTATTGAA Homo sapiens hg19 +ATM10.chr11.108173640.108173640_tile_1 ATM10.chr11.108173640.108173640_tile_1 1 chr11 108173612 108173801 + AAATCTGTGGATTCCTCTAAGTGAAAATCATGACATTTGGATAAAGACACTGACTTGTGCTTTTTTGGACAGTGGAGGCACAAAATGTGAAATTCTTCAATTATTAAAGCCAATGTGTGAAGTAAGAAGATTAATT Homo sapiens hg19 +ATM11.chr11.108180945.108180945_tile_1 ATM11.chr11.108180945.108180945_tile_1 1 chr11 108180915 108181101 + AAGTTGCCAAGGTAGCTCAGTCTTGTGCTGCTCACTTTACAGCTTTACTCTATGCAGAAATCTATGCAGATAAGAAAAGTATGGATGATCAAGAGAAAAGGTAATGGAATTTAGAATTTTTGGTTTTTAAAA Homo sapiens hg19 +ATM12.chr11.108200958.108200961_tile_1 ATM12.chr11.108200958.108200961_tile_1 1 chr11 108200926 108201096 + TTCAGCGAGAGCTGGAGTTGGATGAATTAGCCCTGCGTGCACTGAAAGAGGATCGTAAACGCTTCTTATGTAAAGCAGTTGAAAATTATATCAACTGCTTATTAAGTGGAGAAGA Homo sapiens hg19 +ATM14.chr11.108204681.108204681_tile_1 ATM14.chr11.108204681.108204681_tile_1 1 chr11 108204651 108204823 + TACTATGGAAATTAAGGTAATTTGCAATTAACTCTTGATTTTTTTTAAACTAAATTTTTTTTATTAGATTGAACCATTTGAAATAGTATTTTTATGTAGGTCAAAATTGGTTAAATA Homo sapiens hg19 +ATM15.chr11.108205769.108205769_tile_1 ATM15.chr11.108205769.108205769_tile_1 1 chr11 108205739 108205928 + AGGTGTAAATTTACCAAAAATAATAGATTGTGTAGGTTCCGATGGCAAGGAGAGGAGACAGCTTGTTAAGGTGAGCCTTCCCTTCTCTGGCTTAGCCCTTAGAGTTTTAGTGATGAAAATTTTTAGTTCATATT Homo sapiens hg19 +ATM16.chr11.108206594.108206594_tile_1 ATM16.chr11.108206594.108206594_tile_1 1 chr11 108206566 108206750 + GATGCTGTCATGCAACAGGTCTTCCAGATGTGTAATACATTACTGCAGAGAAACACGGAAACTAGGAAGAGGAAATTAACTATCTGTACTTATAAGGTAACTATTTGTACTTCTGTTAGTTCACCAAAAAC Homo sapiens hg19 +ATM17.chr11.108218089.108218089_tile_1 ATM17.chr11.108218089.108218089_tile_1 1 chr11 108218061 108218247 + TCTAGGTAAGTAATAAAATCTATGTATCTATTCTTTTTAGTAAATATTTGGTCATCATGGAATGTTGTTTGCCTACCAAGATATTACAAATATAAGAGACAGATAAATTGAAGCAGTAAATATTGGGTTTTTT Homo sapiens hg19 +ATM18.chr11.108225590.108225590_tile_1 ATM18.chr11.108225590.108225590_tile_1 1 chr11 108225562 108225751 + AACCATTGTAGAGGTAAAGTATTTTATAAGGAAGACTTTATTTTTTTTCTTACCAGGTAGACTGTGTATCTCATCAGGAAGTCACTGATGTGAAGAGCACTGCTTCATTTTAACATAGGGGGATGTGGCTGGGCAGC Homo sapiens hg19 +ATM19.chr11.108236086.108236203_tile_1 ATM19.chr11.108236086.108236203_tile_1 1 chr11 108236058 108236241 + ACGTGTCTTAATGAGACTACAAGAGAAACTGAAAGGAGTGGAAGAAGGCACTGTGCTCAGTGTTGGTGGACAAGTGAATTTGCTCATACAGCAGGCCATAGACCCCAAAAATCTCAGCCGACTTTTCCCAG Homo sapiens hg19 +KRAS1.chr12.25378562.25378562_tile_1 KRAS1.chr12.25378562.25378562_tile_1 1 chr12 25378532 25378717 + TTGCTGATGTTTCAATAAAAGGAATTCCATAACTTCTTGCTAAGTCCTGAGCCTGTTTTGTGTCTACTGTTCTAGAAGGCAAATCACATTTATTTCCTACTAGGACCATAGGTACATCTTCAGAGTCCTTA Homo sapiens hg19 +KRAS2.chr12.25380275.25380283_tile_1 KRAS2.chr12.25380275.25380283_tile_1 1 chr12 25380245 25380427 + CCTCTTGACCTGCTGTGTCGAGAATATCCAAGAGACAGGTTTCTCCATCAATTACTACTTGCTTCCTGTAGGAATCCTGAGAAGGGAGAAACACAGTCTGGATTATTACAGTGCACCTTTTACTTCAA Homo sapiens hg19 +KRAS7.chr12.25398255.25398285_tile_1 KRAS7.chr12.25398255.25398285_tile_1 1 chr12 25398225 25398414 + TGTATCGTCAAGGCACTCTTGCCTACGCCACCAGCTCCAACTACCACAAGTTTATATTCAGTCATTTTCAGCAGGCCTTATAATAAAAATAATGAAAATGTGACTATATTAGAACATGTCACACATAAGGTTA Homo sapiens hg19 +PTPN11_1.chr12.112888163.112888211_tile_1 PTPN11_1.chr12.112888163.112888211_tile_1 1 chr12 112888135 112888323 + TGGTGATTACTATGACCTGTATGGAGGGGAGAAATTTGCCACTTTGGCTGAGTTGGTCCAGTATTACATGGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTCATTGAGCTTAAATATCCTCTGAACTGT Homo sapiens hg19 +PTPN11_10.chr12.112926884.112926888_tile_1 PTPN11_10.chr12.112926884.112926888_tile_1 1 chr12 112926856 112927032 + GGTCAGGGATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATATTGAAACACTACAGCGCAGGATTGAAGAAGAGCAGGTACCAGCCTGAGGGCTGGCATGCGG Homo sapiens hg19 +HNF1A_1.chr12.121431413.121431414_tile_1 HNF1A_1.chr12.121431413.121431414_tile_1 1 chr12 121431385 121431558 + GTGGGGCCCAGCATCCCAGCAGATCCTGTTCCAGGCCTATGAGAGGCAGAAGAACCCTAGCAAGGAGGAGCGAGAGACGCTAGTGGAGGAGTGCAATAGGTACAACGGCGGGCGGGAAACAG Homo sapiens hg19 +HNF1A_3.chr12.121432070.121432070_tile_1 HNF1A_3.chr12.121432070.121432070_tile_1 1 chr12 121432042 121432221 + GCGCAAAGAAGAAGCCTTCCGGCACAAGCTGGCCATGGACACGTACAGCGGGCCCCCCCCAGGGCCAGGCCCGGGACCTGCGCTGCCCGCTCACAGCTCCCCTGGCCTGCCTCCACCTGCCCTCTCCCCC Homo sapiens hg19 +FLT3_1.chr13.28592620.28592653_tile_1 FLT3_1.chr13.28592620.28592653_tile_1 1 chr13 28592590 28592766 + CATAGTTGGAATCACTCATGATATCTCGAGCCAATCCAAAGTCACATATCTTCACCACTTTCCCGTGGGTGACAAGCACGTTCCTGGCGGCCAGGTCTCTGTGAACACACTGTCAAGAATGA Homo sapiens hg19 +FLT3_13.chr13.28602329.28602329_tile_1 FLT3_13.chr13.28602329.28602329_tile_1 1 chr13 28602295 28602464 + GTGTGCACGCCCCCAGCAGGTTCACAATATTCTCGTGGCTTCCCAGCTGGGTCATCATCTTGAGTTCTGACATGAGTGCCTCTCTTTCAGAGCTGTCTGCTTTTTCTGTCAAAGAA Homo sapiens hg19 +FLT3_14.chr13.28608244.28608341_tile_1 FLT3_14.chr13.28608244.28608341_tile_1 1 chr13 28608214 28608402 + ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTAAATTGCTTCAGAGATGAAATGATGAGTCA Homo sapiens hg19 +FLT3_22.chr13.28610138.28610138_tile_1 FLT3_22.chr13.28610138.28610138_tile_1 1 chr13 28610098 28610267 - TATAGGAGTGAACCACTATGCCCAGCCAGTGAGCTTATTTCACACGTTCTTTTCTATAGGGAAACCTCAAGTGCTCGCAGAAGCATCGGCAAGTCAGGCGTCCTGTTTCTCGGATGG Homo sapiens hg19 +RB1_1.chr13.48919244.48919244_tile_1 RB1_1.chr13.48919244.48919244_tile_1 1 chr13 48919156 48919336 + ATTTACTTTTTTCTATTCTTTCCTTTGTAGTGTCCATAAATTCTTTAACTTACTAAAAGAAATTGATACCAGTACCAAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATGATGTATTG Homo sapiens hg19 +RB1_2.chr13.48923148.48923148_tile_1 RB1_2.chr13.48923148.48923148_tile_1 1 chr13 48923120 48923296 + TTATTAGCTAAAGGTAAGTTCATTATATTTATTAAATGCTAATATTTCAAATGTAATAATTAAATTGGCATTCCTTTGGACTAAATTCCCCAATTTTTATTGAGTAATGTACTCCTCCCTCAT Homo sapiens hg19 +RB1_3.chr13.48942685.48942685_tile_1 RB1_3.chr13.48942685.48942685_tile_1 1 chr13 48942655 48942826 + ACGAAAAAGTAACCTTGATGAAGAGGTGAATGTAATTCCTCCACACACTCCAGTTAGGTATGAATTTTCCTACTTTTAATTATATTATAATTTTGTTATTCATGGCTTTATAGTG Homo sapiens hg19 +RB1_4.chr13.48955538.48955550_tile_1 RB1_4.chr13.48955538.48955550_tile_1 1 chr13 48955504 48955684 + TAGAACGATGTGAACATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGAAATTCATTCATGTGCATATGGCTAACAAATTATTGTTAGTGAGAGGTGTTTCTTA Homo sapiens hg19 +RB1_6.chr13.49027168.49027168_tile_1 RB1_6.chr13.49027168.49027168_tile_1 1 chr13 49027112 49027288 + TTTGATCTTATTAAACAATCAAAGGACCGAGAAGGACCAACTGATCACCTTGAATCTGCTTGTCCTCTTAATCTTCCTCTCCAGAATAATCACACTGCAGCAGATATGTAAGCAAAATATA Homo sapiens hg19 +RB1_7.chr13.49033843.49033846_tile_1 RB1_7.chr13.49033843.49033846_tile_1 1 chr13 49033813 49033989 + TCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATGAGTATGAACTCATGAGAGACAGGCATTT Homo sapiens hg19 +RB1_8.chr13.49037877.49037877_tile_1 RB1_8.chr13.49037877.49037877_tile_1 1 chr13 49037815 49037985 + TTTACATCAATTTATTTACTAGATTATGATGTGTTCCATGTATGGCATATGCAAAGTGAAGAATATAGACCTTAAATTCAAAATCATTGTAACAGCATACAAGGATCTTCCTCA Homo sapiens hg19 +RB1_9.chr13.49039164.49039164_tile_1 RB1_9.chr13.49039164.49039164_tile_1 1 chr13 49039132 49039304 + AAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCCACCAGGGTAGGTCAAAAGTATCCTTTGATTGGAAAA Homo sapiens hg19 +AKT1.chr14.105246455.105246455_tile_1 AKT1.chr14.105246455.105246455_tile_1 1 chr14 105246429 105246600 + CTCACGTTGGTCCACATCCTGCGGCCGCTCCTTGTAGCCAATGAAGGTGCCATCATTCTTGAGGAGGAAGTAGCGTGGCCGCCAGGTCTTGATGTACTCCCCTACAGACGTGCGGGTGGTGA Homo sapiens hg19 +CDH1_1.chr16.68835649.68835650_tile_1 CDH1_1.chr16.68835649.68835650_tile_1 1 chr16 68835613 68835782 + TGGGCACAGATGGTGTGATTACAGTCAAAAGGCCTCTACGGTTTCATAACCCACAGATCCATTTCTTGGTCTACGCCTGGGACTCCACCTACAGAAAGTTTTCCACCAAAGTCACGCTGAAT Homo sapiens hg19 +CDH1_2.chr16.68846137.68846137_tile_1 CDH1_2.chr16.68846137.68846137_tile_1 1 chr16 68846109 68846283 + CGATAATCCTCCGATCTTCAATCCCACCACGGTAATTCTATAACTCCTTAGAGGGTTTCCAAAGAAAGGTCTTTTGTTGTTCATGAACTAAGTGTCACCACTGCTCATGGGCGAAGTCTTT Homo sapiens hg19 +CDH1_3.chr16.68847274.68847277_tile_1 CDH1_3.chr16.68847274.68847277_tile_1 1 chr16 68847246 68847422 + ACTGATGCTGATGCCCCCAATACCCCAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGAACAACGATGGCATTTTGAAAACAGCA Homo sapiens hg19 +TP53_1.chr17.7574003.7574021_tile_1 TP53_1.chr17.7574003.7574021_tile_1 1 chr17 7573977 7574147 + CGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATG Homo sapiens hg19 +TP53_3.chr17.7577022.7577129_tile_1 TP53_3.chr17.7577022.7577129_tile_1 1 chr17 7576996 7577166 + CGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCG Homo sapiens hg19 +TP53_17.chr17.7577523.7577574_tile_1 TP53_17.chr17.7577523.7577574_tile_1 1 chr17 7577495 7577683 + GGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGA Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_1 TP53_31_59.chr17.7578190.7578536_tile_1 1 chr17 7578064 7578234 + AGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTA Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_2 TP53_31_59.chr17.7578190.7578536_tile_2 1 chr17 7578156 7578325 - CTGATTGCTCTTAGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCC Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_3 TP53_31_59.chr17.7578190.7578536_tile_3 1 chr17 7578246 7578415 + TGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCG Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_4 TP53_31_59.chr17.7578190.7578536_tile_4 1 chr17 7578346 7578515 - GTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCG Homo sapiens hg19 +TP53_31_59.chr17.7578190.7578536_tile_5 TP53_31_59.chr17.7578190.7578536_tile_5 1 chr17 7578468 7578645 + CCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGA Homo sapiens hg19 +TP53_60.chr17.7579358.7579403_tile_1 TP53_60.chr17.7579358.7579403_tile_1 1 chr17 7579324 7579507 + GCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAG Homo sapiens hg19 +TP53_64.chr17.7579882.7579882_tile_1 TP53_64.chr17.7579882.7579882_tile_1 1 chr17 7579852 7580032 + GCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAG Homo sapiens hg19 +ERBB2_1.chr17.37880219.37880261_tile_1 ERBB2_1.chr17.37880219.37880261_tile_1 1 chr17 37880191 37880361 + TGTTGAGGGAAAACACATCCCCCAAAGCCAACAAAGAAATCTTAGACGTAAGCCCCTCCACCCTCTCCTGCTAGGAGGACAGGAAGGACCCCATGGCTGCAGGTCTGGGCTCTGGTCT Homo sapiens hg19 +ERBB2_4.chr17.37880993.37881012_tile_1 ERBB2_4.chr17.37880993.37881012_tile_1 1 chr17 37880963 37881151 + CGTGATGGCTGGTGTGGGCTCCCCATATGTCTCCCGCCTTCTGGGCATCTGCCTGACATCCACGGTGCAGCTGGTGACACAGCTTATGCCCTATGGCTGCCTCTTAGACCATGTCCGGGAAAACCGCGGACGCCTGGG Homo sapiens hg19 +ERBB2_13.chr17.37881332.37881440_tile_1 ERBB2_13.chr17.37881332.37881440_tile_1 1 chr17 37881298 37881482 + GCGGCTCGTACACAGGGACTTGGCCGCTCGGAACGTGCTGGTCAAGAGTCCCAACCATGTCAAAATTACAGACTTCGGGCTGGCTCGGCTGCTGGACATTGACGAGACAGAGTACCATGCAGATGGGGGCA Homo sapiens hg19 +SMAD4_1.chr18.48575169.48575170_tile_1 SMAD4_1.chr18.48575169.48575170_tile_1 1 chr18 48575131 48575301 + TTTGACTTAAAATGTGATAGTGTCTGTGTGAATCCATATCACTACGAACGAGTTGTATCACCTGGAATTGGTAAGTAGACTTTGCTTTCATCCTAAGAAACATAAAGGGAAA Homo sapiens hg19 +SMAD4_2.chr18.48581198.48581198_tile_1 SMAD4_2.chr18.48581198.48581198_tile_1 1 chr18 48581168 48581346 + AGGGACAGCCATCGTTGTCCACTGAAGGACATTCAATTCAAACCATCCAGCATCCACCAAGTAATCGTGCATCGACAGAGACATACAGCACCCCAGCTCTGTTAGCCCCATCTGAGTCTAATGC Homo sapiens hg19 +SMAD4_3.chr18.48584560.48584560_tile_1 SMAD4_3.chr18.48584560.48584560_tile_1 1 chr18 48584528 48584714 + GGGCCTCAGCCAGGACAGCAGCAGAATGGATTTACTGGTCAGCCAGCTACTTACCATCATAGTATGTACATACTTTAAAAAATCTTTTAAATAGTTGAGAAAAAAGTAGGCAGCCTTTATAAAAGCAAATTAAC Homo sapiens hg19 +SMAD4_4.chr18.48586262.48586262_tile_1 SMAD4_4.chr18.48586262.48586262_tile_1 1 chr18 48586234 48586416 + CCAGCCTCCCATTTCCAATCATCCTGGTAAGTGTATTTCAAAATTGATTTCCTGTATTTAGATTGATTTAGTGGTGATTGAAACGCACAAACACAGGCTTTAATGGAATTATGGGGTCACTTCTCAGAT Homo sapiens hg19 +SMAD4_5.chr18.48591826.48591919_tile_1 SMAD4_5.chr18.48591826.48591919_tile_1 1 chr18 48591796 48591982 + TTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAATGTCCACAGGAC Homo sapiens hg19 +SMAD4_11.chr18.48593405.48593405_tile_1 SMAD4_11.chr18.48593405.48593405_tile_1 1 chr18 48593377 48593547 + AAGGTGTGCAGTTGGAATGTAAAGGTGAAGGTGATGTTTGGGTCAGGTGCCTTAGTGACCACGCGGTCTTTGTACAGAGTTACTACTTAGACAGAGAAGCTGGGCGTGCACCTGGAGA Homo sapiens hg19 +SMAD4_12.chr18.48603032.48603094_tile_1 SMAD4_12.chr18.48603032.48603094_tile_1 1 chr18 48602998 48603168 + TGTCATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGCCCAGGATCAGTAGGTGGAATAGCTCCA Homo sapiens hg19 +SMAD4_15.chr18.48604668.48604754_tile_1 SMAD4_15.chr18.48604668.48604754_tile_1 1 chr18 48604638 48604808 + CGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTGGGGACCGGATTACCCAAGACAGAGCATCAAAGAAACACCTTGCTGGATTGAAATTCACTTACACCGGGCCCTCCAGC Homo sapiens hg19 +STK11_1.chr19.1207021.1207092_tile_1 STK11_1.chr19.1207021.1207092_tile_1 1 chr19 1206993 1207169 + CCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGTACCTGATGGGGGACCTGCTGGGGGAAGGCTCTTACGGCAAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGCAGGAGGGCCGT Homo sapiens hg19 +STK11_4.chr19.1220487.1220502_tile_1 STK11_4.chr19.1220487.1220502_tile_1 1 chr19 1220459 1220638 + CCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTTCGCGGCGGACGACACCTGCCG Homo sapiens hg19 +STK11_8.chr19.1221264.1221319_tile_1 STK11_8.chr19.1221264.1221319_tile_1 1 chr19 1221232 1221407 - CCCGCCTCCCTGGGGCTGCGGGCAGAGGGATGAGGCTCCCACCTTTCAGCAGGTCAGAGAGCGGGGGGCCACAGTCGCCCGGGATGGCGTAGCTCCCCTTCCCGATGTTCTCAAACAACTTG Homo sapiens hg19 +STK11_12.chr19.1223059.1223125_tile_1 STK11_12.chr19.1223059.1223125_tile_1 1 chr19 1223035 1223221 + GGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCC Homo sapiens hg19 +JAK3_1.chr19.17945696.17945696_tile_1 JAK3_1.chr19.17945696.17945696_tile_1 1 chr19 17945666 17945840 + GGTGACGCCACTAAACACTTCCCAGACCGTGGCGCCGAAGCCCCACTTGTCAGCTTCCAAGCTAAGTGTCTGCGCCTCCCGGAGACACTCGGGGGCCACCCAGGGGATCCTGTCGGTGAGCAC Homo sapiens hg19 +JAK3_2.chr19.17948009.17948009_tile_1 JAK3_2.chr19.17948009.17948009_tile_1 1 chr19 17947981 17948169 + CGCTGCTTCCAGGAATGACTGGGGAAGGTGGGAAGGGAGAGAAGATGCGTGGGTTTCTTCCACTCCAATAATCCCAAATTTTGTGCTCACAGACCTGCCTTAGGGGAACACCTGGCCACAGGTCACCTTTGGCCCTGG Homo sapiens hg19 +SRC.chr20.36031762.36031762_tile_1 SRC.chr20.36031762.36031762_tile_1 1 chr20 36031734 36031923 + CCAGCCCGGGGAGAACCTCTAGGCACAGGCGGGCCCAGACCGGCTTCTCGGCTTGGATCCTGGGCTGGGTGGCCCCTGTCTCGGGGCTTGCCCCACTCTGCCTGCCTGCTGTTGGTCCTCTCTCTGTGGGGCTGA Homo sapiens hg19 +GNAS1.chr20.57484420.57484421_tile_1 GNAS1.chr20.57484420.57484421_tile_1 1 chr20 57484390 57484560 + TGCCGTGTCCTGACTTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCAGTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCAC Homo sapiens hg19 +SMARCB1_1.chr22.24133967.24133990_tile_1 SMARCB1_1.chr22.24133967.24133990_tile_1 1 chr22 24133939 24134126 + TCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGGAGGCGACTAGCCACTGTGGAAGAGAGGAAGAAAATAGTTGCATCGTCACATGGTAAAAAAACAAAACCTAACACTAAGGGTGCGTCTTCACGAGGGTT Homo sapiens hg19 +SMARCB1_3.chr22.24143240.24143240_tile_1 SMARCB1_3.chr22.24143240.24143240_tile_1 1 chr22 24143210 24143383 + GGGCCGAGACAAGAAGAGAACCTTCCCCCTTTGGTGTGGATGCATCGCTGCACTCACCCTCCGTGCTGATTCCGCCTTAGTTCTCCAGCACGTTTCAGTTCCTTCCTCCCCAGAAAAACACT Homo sapiens hg19 +SMARCB1_4.chr22.24145582.24145582_tile_1 SMARCB1_4.chr22.24145582.24145582_tile_1 1 chr22 24145552 24145726 + GCTGCGAGACGCCTTCACCTGGAACATGAATGGTACAAGGCAGTCGGGCTTGGCTGGGCCTGGCCCCAACCCCTGTGTGTTACGTGGGAACAGTCCCGTTTCCTGCCAGCTGCCTGTCAGGC Homo sapiens hg19 +SMARCB1_5_6.chr22.24176352.24176357_tile_1 SMARCB1_5_6.chr22.24176352.24176357_tile_1 1 chr22 24176324 24176495 + CGGCCCCGGCCTGGTAACCAGCCCATCAGCACACGGCTCCCACGGAGCATCTCAGAAGATTGGGCCGCCTCTCCTCCATCTTCTGGCAAGGACAGAGGCGAGGGGACAGCCCAGCGCCA Homo sapiens hg19 +GNA11_4.chr19.3114942.3115070_tile_1 GNA11_4.chr19.3114942.3115070_tile_1 1 chr19 3114824 3115004 - GTAGCCCAAGGTGGCGATGCGGTCAACGTCGGTCAGGTAGCTGCAACACAGCGGTGGGTGCTCAGGCCGGCTGCCGGGGGTGGGGGGGCAGGACAGGGACACAGCACCCAAACCAGCGGGAGGACGGAAAGCCACC Homo sapiens hg19 +GNA11_4.chr19.3114942.3115070_tile_2 GNA11_4.chr19.3114942.3115070_tile_2 1 chr19 3114958 3115133 + CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCATCATCGAGTACCCTTTCGACCTGGAGAACATCATCTTCCGGTACCGCCCGGGCCACAGCAGGCGGGGAGGGGGCACTGAGA Homo sapiens hg19 +GNA11_5.chr19.3118922.3119051_tile_1 GNA11_5.chr19.3118922.3119051_tile_1 1 chr19 3118802 3118989 - CACTTCCTCCGCTCCGACCGCTGGCCCCCCACATCCACCATCCTGAAAGGACACAGCGCCAGGACTCAGCCACCTGGCGCCCCAAGGCCCAATCTGCAATCCCAGGACGGCTCCCACCCAAGCCCCTCCTGCCACACC Homo sapiens hg19 +GNA11_6.chr19.3119204.3119357_tile_2 GNA11_6.chr19.3119204.3119357_tile_2 1 chr19 3119208 3119395 - CCGCAGCCCGGCGCACCATCGAACTCGGGGAAGTAGTCCACCAGGTGCGAGTACAGGATCTTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGAGGATGACGGAGGAGTTCTGGAACCAGGGGTAGGTGATGATGGTCCGG Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_1 GNA11_7.chr19.3120987.3121177_tile_1 1 chr19 3120865 3121035 + GGGCCTTACTCGCTCATCCCCTGGGAGTGACAAAGGGGCCCACGAGTCCCTTGCCCTGGGCCGGGCTGGGGCACAGCCTCACCCTCTGCCCTCCCCCAGGTCCCCAGCGGGACGCCCAGGC Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 1 chr19 3120985 3121170 - CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTCCGTGTCGGTGGCACACGTGAAGTGTGAGTAGATGATCTTGTCGCTGTCGGGGTTCAGGTCCACGAACATCTTCAGGATGAACTCCCGCGCCGC Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_3 GNA11_7.chr19.3120987.3121177_tile_3 1 chr19 3121121 3121304 + GCAGCTCAACCTCAAGGAGTACAACCTGGTCTGAGCGCCCAGGCCCAGGGAGACGGGATGGAGACACGGGGCAGGACCTTCCTTCCACGGAGCCTGCGGCTGCCGGGCGGGTGGCGCTGCCGAGTCCGGGCCGGGGC Homo sapiens hg19 +GNAQ_4.chr9.80412436.80412564_tile_1 GNAQ_4.chr9.80412436.80412564_tile_1 1 chr9 80412406 80412592 + TACCTGAAAATGACACTTTGTAAGTCAAAGGGGTATTCGATGATCCCTGTGGTGGGGACTCGAACTCTAAGCACATCTTGTTGCGTAGGCAGGTAGGCAGGGTCAGCTACGCGGTCCAAGTCATTAAGATAGC Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_5.chr9.80409379.80409508_tile_1 1 chr9 80409249 80409421 + AAAGAAGTAAGTTCACTCCATTCCCCACACCCTACTTTCTATCATTTACTTGTATCAGATAATAAAATGATAATCCATTGCCTGTCTAAAGAACACTTACCTCATTGTCTGACT Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 1 chr9 80409335 80409510 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCAAGTTCTCGTGGAGTCAGACAATGAGGTAAGTGTTCTTTA Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_3 GNAQ_5.chr9.80409379.80409508_tile_3 1 chr9 80409459 80409639 + TTTGGCCCCCTACATCGACCATTCTGCAAGGTTAACAATACTCATATTAATAACATATAAAGTAAAACTAAAAAGTCAACATAAATATAGCACTACTTACAAACTTAGGGAAAATATTCTCTTGAAT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_6.chr9.80343430.80343583_tile_1 1 chr9 80343306 80343476 + GGGCAGCAATGGTGCACTGTAGTGCGTTAACTCCCACACTGGGGTTTGGAGACAAAACCTATTCACAGCTACTGAGCTGTGGTATGAGTGCTGACTTACCATCATATTCTGGGAAGT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_2 GNAQ_6.chr9.80343430.80343583_tile_2 1 chr9 80343392 80343561 - GGTTCCAGAACTCCTCGGTTATTCTGTTCTTAAACAAGAAAGATCTTCTAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGTAAGTCAGCAC Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_3 GNAQ_6.chr9.80343430.80343583_tile_3 1 chr9 80343504 80343689 + CAGGGGTATGTGATAATTGTTCTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTGGAAAAAAAAAAAAAATCAGAAAAAACAAGGAGTGAATTACATGATTACTTAATTTGTGAATTGTGTTTATTTT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 1 chr9 80336110 80336280 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCAGGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAATTAGACCAGATTGTACT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_7.chr9.80336240.80336429_tile_2 1 chr9 80336204 80336374 - CTACTCCCACTTCACGTGCGCCACAGACACCGAGAATATCCGCTTTGTCTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGAGTACAATCTGGTCTAATTGTGCCTCC Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_3 GNAQ_7.chr9.80336240.80336429_tile_3 1 chr9 80336320 80336495 + GATAATTTTGTCACTGTCTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCTTTCGGCCAAGAGACAAGAGGGACACTTTGTTACCTA Homo sapiens hg19 +PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 2 chr22 17052964 17053133 + ATCCTCTCTCTGAAATCACTGCGCAGGAGAAAGATTTTCTATGGACCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGACTTTGG Homo sapiens hg19 +PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 2 chr22 17055413 17055585 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTGTCAAACAGGAGAAGAAGGATGAAACACAAAAGTTGTGTGACTCTAGTCTGTGTTTGAGACTCTT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN3.chr10.89685307.89685307_tile_1 2 chr9 33675957 33676480 - ATACACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATCTAATTACAGAGTTGCGCAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTATAATGATTTATGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 2 chr9 33675629 33675815 - CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAGTATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 +GNA11_6.chr19.3119204.3119357_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 2 chr7 65970150 65970483 + CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTTCGTGTCGGTGGCGTACGTGAAGTGGGAGTCGATGATCTTGTCGCTGTCGGGGTTCATGTCCACTAACATCTTCAGGATGAACTCCCGCGCCGCCTGGGCGTCCTGCTGGGGCCCTTCGAACTCGGGGAAGTAGTCCACCATGTGTGAGTACAGGATATTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGGTGATGACGGGGGAGTTCTGGAACCAGGGGTAGTCGATGATGGTCCGG Homo sapiens hg19 +GNA11_7.chr19.3120987.3121177_tile_1 GNA11_4.chr19.3114942.3115070_tile_2 2 chr7 65970285 65970719 - CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCGTCTTTCGACCTGGAGAACATCATCTTCAGGATGGCGGATGTTGGGGGACAGCGGTCGGCGCAGAGGAAGTGGATCCACTGCTTTGAGAACCTGACGTCCATCCCGTTTCTCGTCGCCCTCAGTGAATACGACCAAGTCCTGGTGGAGTCGGACAACGAGAACCGGATGGAGGAGAGCAAAGCCCTGTTCCGGACCATCATCGACTACCCCTGGTTCCAGAACTCCCCCGTCATCACCTTCCTCAACAAGAAGGACCTGCTGGAGGACAATATCCTGTACTCACACATGGTGGACTACTTCCCCGAGTTCGAAGGGCCCCAGCAGGACGCCCAGGC Homo sapiens hg19 +GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 2 chr2 132181238 132181750 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCATGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAACTAGACCAGATTGTAATCCTTCAGGTTCAACTGGAGGATGGTGTCCTTGACGGCAGCAAACACAAAGCGGATATTCTCGGTGTCTGTGGCGCATGTGAAGTGGGAGTAGATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGTAGTCGACTAGATGGGAATACATGATTTTCTCCTCTGGAAGATCTTTCTTGTTTAACAACAGAATAACCGAGGAGTTCTGGAACCAGGGATACGTGATAATTGTACTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTCATTGTCTGACT Homo sapiens hg19 +GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_7.chr9.80336240.80336429_tile_3 2 chr2 132181448 132181600 + GATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGT Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 2 chr2 132181332 132181839 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCGAGTTCTCGTGGAGTCAGACAATGAGAACCGAATGGAGGAAAGCAAGGCTCTCTTTAGTACAATTATCACGTATCCCTGGTTCCAGAACTCCTCGGTTATTCTGTTGTTAAACAAGAAAGATCTTCCAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGACCCCAGAGAGATGCCCAGGCAGCCCGAGAATTCATTCTGAAGATGTTCGTGGACCTGAACCCAGTGACCAAATTATCTACTCCCACTTCACATGCGCCACAGACACCGAGAATATCCGCTTTGTGTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGATTACAATCTGGTCTAGTTGTGCCTCC Homo sapiens hg19 +GNAQ_7.chr9.80336240.80336429_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 2 chr2 132181238 132181408 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCATGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAACTAGACCAGATTGTAAT Homo sapiens hg19 +IDH1_1_2.chr2.209113112.209113113_tile_1 IDH1_1_2.chr2.209113112.209113113_tile_1 2 chr6 7517651 7517831 + GCGACCTACGATGATGGATTTTACCCATCCACTCACAAGCTGGGGGATATTTTTGCAGATAATGGCTTCTCTGAGGACCGTGCCAACCAGAATATTTTGGATGGTGCCATTTGGCGATTTCCACATT Homo sapiens hg19 +PTEN7.chr10.89717615.89717772_tile_1 PTEN4.chr10.89711893.89711900_tile_1 2 chr9 33675957 33676167 - GTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 +PTEN13.chr10.89720716.89720852_tile_1 PTEN4.chr10.89711893.89711900_tile_1 2 chr9 33675629 33676167 - GTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATGTATTCCTCCAATTCAGGACCCACACGATGGGAGGACAAGTTCATGTATTTTGAGTTCCCTCAGCCGTTACCTGTGTGTGGTGATATCAAAGTAGAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAGTATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/filters/README Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,1 @@ +Filters are made from dbSNP, both clinical and with no known medical impact and from cosmic, both coding and non-coding. Only chromocol coordinates are recorded in the file.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/ref/filters/filter.tsv Tue Dec 23 11:26:33 2014 -0500 @@ -0,0 +1,5917 @@ +1 43814984 +1 43814990 +1 43814992 +1 43814994 +1 43815004 +1 43815006 +1 43815007 +1 43815008 +1 43815009 +1 43815020 +1 43815021 +1 43815024 +1 43815035 +1 115256507 +1 115256508 +1 115256509 +1 115256516 +1 115256518 +1 115256521 +1 115256524 +1 115256526 +1 115256527 +1 115256528 +1 115256529 +1 115256530 +1 115256532 +1 115256534 +1 115256535 +1 115256536 +1 115256537 +1 115256538 +1 115256539 +1 115256562 +1 115256564 +1 115256566 +1 115256577 +1 115256591 +1 115256669 +1 115258712 +1 115258718 +1 115258722 +1 115258723 +1 115258727 +1 115258728 +1 115258730 +1 115258732 +1 115258734 +1 115258736 +1 115258738 +1 115258739 +1 115258742 +1 115258743 +1 115258744 +1 115258745 +1 115258746 +1 115258747 +1 115258748 +1 115258751 +1 115258752 +1 115258753 +1 115258754 +1 115258757 +1 115258771 +2 29432652 +2 29432655 +2 29432658 +2 29432663 +2 29432664 +2 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--- a/tool-data/GALAXY_TSACP.bed Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,221 +0,0 @@ -chr1 43814981 43815163 MPL1_2.chr1.43815008.43815009_tile_1 100 + 43815005 43815137 -chr1 115256499 115256680 NRAS1_7.chr1.115256528.115256531_tile_1 100 + 115256525 115256653 -chr1 115258701 115258884 NRAS8_13.chr1.115258730.115258748_tile_1 100 + 115258727 115258855 -chr2 29432635 29432822 ALK1.chr2.29432664.29432664_tile_1 100 + 29432662 29432795 -chr2 29443666 29443836 ALK2.chr2.29443695.29443695_tile_1 100 + 29443691 29443810 -chr2 209113083 209113264 IDH1_1_2.chr2.209113112.209113113_tile_1 100 + 209113110 209113237 -chr2 212288911 212289100 ERBB4_1_2.chr2.212288942.212288955_tile_1 100 + 212288938 212289073 -chr2 212530035 212530210 ERBB4_3_4.chr2.212530066.212530135_tile_1 100 + 212530061 212530183 -chr2 212576820 212576990 ERBB4_5.chr2.212576857.212576857_tile_1 100 + 212576850 212576960 -chr2 212578314 212578499 ERBB4_6_7.chr2.212578341.212578349_tile_1 100 + 212578339 212578470 -chr2 212587114 212587285 ERBB4_8.chr2.212587147.212587147_tile_1 100 + 212587141 212587258 -chr2 212589782 212589957 ERBB4_9.chr2.212589811.212589811_tile_1 100 + 212589809 212589930 -chr2 212652705 212652876 ERBB4_10.chr2.212652764.212652764_tile_1 100 + 212652735 212652849 -chr2 212812126 212812311 ERBB4_11.chr2.212812157.212812157_tile_1 100 + 212812155 212812284 -chr3 10183768 10183952 VHL1_2.chr3.10183797.10183817_tile_1 100 + 10183793 10183926 -chr3 10188216 10188401 VHL3_5.chr3.10188245.10188301_tile_1 100 + 10188243 10188374 -chr3 10191449 10191634 VHL6_8.chr3.10191480.10191506_tile_1 100 + 10191477 10191607 -chr3 37067211 37067394 MLH1.chr3.37067240.37067240_tile_1 100 + 37067237 37067367 -chr3 41266009 41266180 CTNNB1_1_16.chr3.41266040.41266137_tile_1 100 + 41266036 41266153 -chr3 178916835 178917024 PIK3CA1.chr3.178916876.178916876_tile_1 100 + 178916861 178916997 -chr3 178921524 178921709 PIK3CA2.chr3.178921553.178921553_tile_1 100 + 178921551 178921682 -chr3 178927905 178928082 PIK3CA3.chr3.178927980.178927980_tile_1 100 + 178927932 178928055 -chr3 178936043 178936214 PIK3CA4_11.chr3.178936074.178936095_tile_1 100 + 178936070 178936187 -chr3 178938831 178939004 PIK3CA12.chr3.178938860.178938860_tile_1 100 + 178938858 178938977 -chr3 178951880 178952054 PIK3CA13_20.chr3.178952007.178952150_tile_1 100 + 178951906 178952026 -chr3 178951998 178952184 PIK3CA13_20.chr3.178952007.178952150_tile_2 100 - 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133748186 133748302 -chr9 133748276 133748457 ABL1_10.chr9.133748283.133748414_tile_2 100 + 133748301 133748434 -chr9 133750327 133750516 ABL1_16.chr9.133750356.133750356_tile_1 100 + 133750351 133750489 -chr9 139397739 139397928 NOTCH1_1.chr9.139397768.139397768_tile_1 100 + 139397765 139397901 -chr9 139399315 139399485 NOTCH1_2.chr9.139399344.139399422_tile_1 100 + 139399341 139399459 -chr10 43609047 43609226 RET1.chr10.43609078.43609104_tile_1 100 + 43609073 43609201 -chr10 43609901 43610075 RET2_9.chr10.43609940.43609950_tile_1 100 - 43609929 43610049 -chr10 43613809 43613998 RET10.chr10.43613840.43613840_tile_1 100 + 43613832 43613971 -chr10 43615532 43615703 RET11_12.chr10.43615567.43615569_tile_1 100 + 43615560 43615678 -chr10 43617387 43617564 RET13.chr10.43617416.43617416_tile_1 100 + 43617414 43617537 -chr10 89624213 89624388 PTEN1.chr10.89624242.89624244_tile_1 100 + 89624240 89624361 -chr10 89685274 89685459 PTEN3.chr10.89685307.89685307_tile_1 100 + 89685303 89685432 -chr10 89711864 89712039 PTEN4.chr10.89711893.89711900_tile_1 100 + 89711890 89712012 -chr10 89717488 89717668 PTEN7.chr10.89717615.89717772_tile_1 100 + 89717514 89717638 -chr10 89717614 89717801 PTEN7.chr10.89717615.89717772_tile_2 100 - 89717637 89717772 -chr10 89720683 89720870 PTEN13.chr10.89720716.89720852_tile_1 100 + 89720708 89720843 -chr10 89720813 89720991 PTEN13.chr10.89720716.89720852_tile_2 100 - 89720842 89720961 -chr10 123258005 123258184 FGFR2_1.chr10.123258034.123258034_tile_1 100 + 123258032 123258157 -chr10 123274745 123274930 FGFR2_2.chr10.123274774.123274803_tile_1 100 + 123274772 123274903 -chr10 123279384 123279555 FGFR2_5.chr10.123279503.123279677_tile_1 100 + 123279411 123279528 -chr10 123279470 123279640 FGFR2_5.chr10.123279503.123279677_tile_2 100 - 123279498 123279614 -chr10 123279586 123279769 FGFR2_5.chr10.123279503.123279677_tile_3 100 + 123279613 123279742 -chr11 533842 534021 HRAS1.chr11.533873.533875_tile_1 100 + 533868 533994 -chr11 534250 534434 HRAS6.chr11.534285.534289_tile_1 100 + 534277 534410 -chr11 108117816 108117989 ATM1.chr11.108117847.108117848_tile_1 100 + 108117845 108117962 -chr11 108119792 108119963 ATM2.chr11.108119823.108119823_tile_1 100 + 108119819 108119936 -chr11 108123512 108123683 ATM3.chr11.108123551.108123551_tile_1 100 + 108123541 108123654 -chr11 108137938 108138126 ATM4.chr11.108137973.108138003_tile_1 100 + 108137967 108138096 -chr11 108155103 108155281 ATM6.chr11.108155132.108155132_tile_1 100 + 108155130 108155251 -chr11 108170441 108170618 ATM7.chr11.108170476.108170479_tile_1 100 + 108170468 108170591 -chr11 108172390 108172571 ATM9.chr11.108172421.108172421_tile_1 100 + 108172417 108172544 -chr11 108173611 108173801 ATM10.chr11.108173640.108173640_tile_1 100 + 108173635 108173771 -chr11 108180914 108181101 ATM11.chr11.108180945.108180945_tile_1 100 + 108180942 108181074 -chr11 108200925 108201096 ATM12.chr11.108200958.108200961_tile_1 100 + 108200954 108201069 -chr11 108204650 108204823 ATM14.chr11.108204681.108204681_tile_1 100 + 108204679 108204796 -chr11 108205738 108205928 ATM15.chr11.108205769.108205769_tile_1 100 + 108205766 108205900 -chr11 108206565 108206750 ATM16.chr11.108206594.108206594_tile_1 100 + 108206592 108206723 -chr11 108218060 108218247 ATM17.chr11.108218089.108218089_tile_1 100 + 108218087 108218220 -chr11 108225561 108225751 ATM18.chr11.108225590.108225590_tile_1 100 + 108225588 108225725 -chr11 108236057 108236241 ATM19.chr11.108236086.108236203_tile_1 100 + 108236084 108236215 -chr12 25378531 25378717 KRAS1.chr12.25378562.25378562_tile_1 100 + 25378558 25378689 -chr12 25380244 25380427 KRAS2.chr12.25380275.25380283_tile_1 100 + 25380270 25380398 -chr12 25398224 25398414 KRAS7.chr12.25398255.25398285_tile_1 100 + 25398253 25398386 -chr12 112888134 112888323 PTPN11_1.chr12.112888163.112888211_tile_1 100 + 112888160 112888296 -chr12 112926855 112927032 PTPN11_10.chr12.112926884.112926888_tile_1 100 + 112926881 112927005 -chr12 121431384 121431558 HNF1A_1.chr12.121431413.121431414_tile_1 100 + 121431410 121431532 -chr12 121432041 121432221 HNF1A_3.chr12.121432070.121432070_tile_1 100 + 121432065 121432195 -chr13 28592589 28592766 FLT3_1.chr13.28592620.28592653_tile_1 100 + 28592617 28592739 -chr13 28602294 28602464 FLT3_13.chr13.28602329.28602329_tile_1 100 + 28602320 28602436 -chr13 28608213 28608402 FLT3_14.chr13.28608244.28608341_tile_1 100 + 28608242 28608375 -chr13 28610097 28610267 FLT3_22.chr13.28610138.28610138_tile_1 100 - 28610122 28610239 -chr13 48919155 48919336 RB1_1.chr13.48919244.48919244_tile_1 100 + 48919185 48919309 -chr13 48923119 48923296 RB1_2.chr13.48923148.48923148_tile_1 100 + 48923146 48923269 -chr13 48942654 48942826 RB1_3.chr13.48942685.48942685_tile_1 100 + 48942683 48942798 -chr13 48955503 48955684 RB1_4.chr13.48955538.48955550_tile_1 100 + 48955532 48955657 -chr13 49027111 49027288 RB1_6.chr13.49027168.49027168_tile_1 100 + 49027140 49027261 -chr13 49033812 49033989 RB1_7.chr13.49033843.49033846_tile_1 100 + 49033839 49033962 -chr13 49037814 49037985 RB1_8.chr13.49037877.49037877_tile_1 100 + 49037844 49037958 -chr13 49039131 49039304 RB1_9.chr13.49039164.49039164_tile_1 100 + 49039158 49039277 -chr14 105246428 105246600 AKT1.chr14.105246455.105246455_tile_1 100 + 105246452 105246574 -chr16 68835612 68835782 CDH1_1.chr16.68835649.68835650_tile_1 100 + 68835638 68835760 -chr16 68846108 68846283 CDH1_2.chr16.68846137.68846137_tile_1 100 + 68846135 68846256 -chr16 68847245 68847422 CDH1_3.chr16.68847274.68847277_tile_1 100 + 68847272 68847395 -chr17 7573976 7574147 TP53_1.chr17.7574003.7574021_tile_1 100 + 7574001 7574120 -chr17 7576995 7577166 TP53_3.chr17.7577022.7577129_tile_1 100 + 7577020 7577139 -chr17 7577494 7577683 TP53_17.chr17.7577523.7577574_tile_1 100 + 7577521 7577656 -chr17 7578063 7578234 TP53_31_59.chr17.7578190.7578536_tile_1 100 + 7578091 7578207 -chr17 7578155 7578325 TP53_31_59.chr17.7578190.7578536_tile_2 100 - 7578180 7578303 -chr17 7578245 7578415 TP53_31_59.chr17.7578190.7578536_tile_3 100 + 7578273 7578389 -chr17 7578345 7578515 TP53_31_59.chr17.7578190.7578536_tile_4 100 - 7578373 7578491 -chr17 7578467 7578645 TP53_31_59.chr17.7578190.7578536_tile_5 100 + 7578490 7578619 -chr17 7579323 7579507 TP53_60.chr17.7579358.7579403_tile_1 100 + 7579350 7579481 -chr17 7579851 7580032 TP53_64.chr17.7579882.7579882_tile_1 100 + 7579878 7580005 -chr17 37880190 37880361 ERBB2_1.chr17.37880219.37880261_tile_1 100 + 37880216 37880334 -chr17 37880962 37881151 ERBB2_4.chr17.37880993.37881012_tile_1 100 + 37880986 37881124 -chr17 37881297 37881482 ERBB2_13.chr17.37881332.37881440_tile_1 100 + 37881324 37881455 -chr18 48575130 48575301 SMAD4_1.chr18.48575169.48575170_tile_1 100 + 48575160 48575272 -chr18 48581167 48581346 SMAD4_2.chr18.48581198.48581198_tile_1 100 + 48581195 48581319 -chr18 48584527 48584714 SMAD4_3.chr18.48584560.48584560_tile_1 100 + 48584553 48584687 -chr18 48586233 48586416 SMAD4_4.chr18.48586262.48586262_tile_1 100 + 48586260 48586389 -chr18 48591795 48591982 SMAD4_5.chr18.48591826.48591919_tile_1 100 + 48591822 48591955 -chr18 48593376 48593547 SMAD4_11.chr18.48593405.48593405_tile_1 100 + 48593402 48593520 -chr18 48602997 48603168 SMAD4_12.chr18.48603032.48603094_tile_1 100 + 48603025 48603139 -chr18 48604637 48604808 SMAD4_15.chr18.48604668.48604754_tile_1 100 + 48604663 48604781 -chr19 1206992 1207169 STK11_1.chr19.1207021.1207092_tile_1 100 + 1207019 1207142 -chr19 1220458 1220638 STK11_4.chr19.1220487.1220502_tile_1 100 + 1220484 1220614 -chr19 1221231 1221407 STK11_8.chr19.1221264.1221319_tile_1 100 - 1221259 1221381 -chr19 1223034 1223221 STK11_12.chr19.1223059.1223125_tile_1 100 + 1223057 1223196 -chr19 17945665 17945840 JAK3_1.chr19.17945696.17945696_tile_1 100 + 17945690 17945813 -chr19 17947980 17948169 JAK3_2.chr19.17948009.17948009_tile_1 100 + 17948004 17948142 -chr20 36031733 36031923 SRC.chr20.36031762.36031762_tile_1 100 + 36031760 36031895 -chr20 57484389 57484560 GNAS1.chr20.57484420.57484421_tile_1 100 + 57484416 57484533 -chr22 24133938 24134126 SMARCB1_1.chr22.24133967.24133990_tile_1 100 + 24133964 24134100 -chr22 24143209 24143383 SMARCB1_3.chr22.24143240.24143240_tile_1 100 + 24143235 24143357 -chr22 24145551 24145726 SMARCB1_4.chr22.24145582.24145582_tile_1 100 + 24145577 24145699 -chr22 24176323 24176495 SMARCB1_5_6.chr22.24176352.24176357_tile_1 100 + 24176350 24176469 -chr19 3114823 3115004 GNA11_4.chr19.3114942.3115070_tile_1 100 - 3114845 3114981 -chr19 3114957 3115133 GNA11_4.chr19.3114942.3115070_tile_2 100 + 3114980 3115111 -chr19 3118801 3118989 GNA11_5.chr19.3118922.3119051_tile_1 100 - 3118825 3118963 -chr19 3119207 3119395 GNA11_6.chr19.3119204.3119357_tile_2 100 - 3119232 3119373 -chr19 3120864 3121035 GNA11_7.chr19.3120987.3121177_tile_1 100 + 3120887 3121008 -chr19 3120984 3121170 GNA11_7.chr19.3120987.3121177_tile_2 100 - 3121006 3121144 -chr19 3121120 3121304 GNA11_7.chr19.3120987.3121177_tile_3 100 + 3121143 3121280 -chr9 80412405 80412592 GNAQ_4.chr9.80412436.80412564_tile_1 100 + 80412432 80412565 -chr9 80409248 80409421 GNAQ_5.chr9.80409379.80409508_tile_1 100 + 80409278 80409392 -chr9 80409334 80409510 GNAQ_5.chr9.80409379.80409508_tile_2 100 - 80409364 80409486 -chr9 80409458 80409639 GNAQ_5.chr9.80409379.80409508_tile_3 100 + 80409485 80409612 -chr9 80343305 80343476 GNAQ_6.chr9.80343430.80343583_tile_1 100 + 80343330 80343447 -chr9 80343391 80343561 GNAQ_6.chr9.80343430.80343583_tile_2 100 - 80343417 80343531 -chr9 80343503 80343689 GNAQ_6.chr9.80343430.80343583_tile_3 100 + 80343530 80343659 -chr9 80336109 80336280 GNAQ_7.chr9.80336240.80336429_tile_1 100 + 80336139 80336255 -chr9 80336203 80336374 GNAQ_7.chr9.80336240.80336429_tile_2 100 - 80336228 80336347 -chr9 80336319 80336495 GNAQ_7.chr9.80336240.80336429_tile_3 100 + 80336346 80336467 -chr22 17052963 17053133 PIK3CA4_11.chr3.178936074.178936095_tile_1 100 + 17052990 17053106 -chr22 17055412 17055585 PIK3CA12.chr3.178938860.178938860_tile_1 100 + 17055439 17055558 -chr9 33675956 33676480 PTEN7.chr10.89717615.89717772_tile_1 100 - 33675986 33676451 -chr9 33675628 33675815 PTEN13.chr10.89720716.89720852_tile_1 100 - 33675655 33675790 -chr7 65970149 65970483 GNA11_6.chr19.3119204.3119357_tile_2 100 + 65970175 65970458 -chr7 65970284 65970719 GNA11_7.chr19.3120987.3121177_tile_1 100 - 65970311 65970696 -chr2 132181237 132181750 GNAQ_5.chr9.80409379.80409508_tile_1 100 + 132181267 132181721 -chr2 132181447 132181600 GNAQ_6.chr9.80343430.80343583_tile_1 100 + 132181474 132181571 -chr2 132181331 132181839 GNAQ_7.chr9.80336240.80336429_tile_2 100 - 132181356 132181815
--- a/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt Fri Oct 10 11:28:57 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,445 +0,0 @@ -[Header] -Customer Name "ILLUMINA, INC." -Product Type 15032433 -Date Manufactured -Lot -DesignStudio ID NA -Target Plexity 212 - -[Probes] -Target Region Name Target Region ID Target ID Species Build ID Chromosome Start Position End Position Submitted Target Region Strand ULSO Sequence ULSO Genomic Hits DLSO Sequence DLSO Genomic Hits Probe Strand Designer Design Score Expected Amplifed Region Size SNP Masking Labels -MPL1_2 MPL1_2.chr1.43815008.43815009 MPL1_2.chr1.43815008.43815009_tile_1 Homo sapiens hg19 chr1 43815008 43815009 - AAGTGGCGAAGCCGTAGGTGCGCACG 0 TCAGCAGCAGCAGGCCCAGGACGG 0 - ILLUMINA NA 183 TRUE -NRAS1_7 NRAS1_7.chr1.115256528.115256531 NRAS1_7.chr1.115256528.115256531_tile_1 Homo sapiens hg19 chr1 115256528 115256531 - CAATAGCATTGCATTCCCTGTGGTTTT 0 AGAGTACAGTGCCATGAGAGACCAAT 0 - ILLUMINA NA 182 TRUE -NRAS8_13 NRAS8_13.chr1.115258730.115258748 NRAS8_13.chr1.115258730.115258748_tile_1 Homo sapiens hg19 chr1 115258730 115258748 - GGGTTTTCATTTCCATTGATTATAGAAAG 0 CTGACAATCCAGCTAATCCAGAACCA 0 - ILLUMINA NA 184 TRUE -ALK1 ALK1.chr2.29432664.29432664 ALK1.chr2.29432664.29432664_tile_1 Homo sapiens hg19 chr2 29432664 29432664 - GATAAAATCCTAGTGATGGCCGTTGTA 0 GACATCTACAGGTGAGTAAAGACTGCC 0 - ILLUMINA NA 188 TRUE -ALK2 ALK2.chr2.29443695.29443695 ALK2.chr2.29443695.29443695_tile_1 Homo sapiens hg19 chr2 29443695 29443695 - TGCTGCCCATGTTTACAGAATGCCTT 0 CACCAGAACATTGTTCGCTGCATTG 0 - ILLUMINA NA 171 TRUE -IDH1_1_2 IDH1_1_2.chr2.209113112.209113113 IDH1_1_2.chr2.209113112.209113113_tile_1 Homo sapiens hg19 chr2 209113112 209113113 - GAGGGTTGAGGAGTTCAAGTTGAAACA 0 CATGCTTATGGGGATCAAGTAAGTCAT 0 - ILLUMINA NA 182 TRUE -ERBB4_1_2 ERBB4_1_2.chr2.212288942.212288955 ERBB4_1_2.chr2.212288942.212288955_tile_1 Homo sapiens hg19 chr2 212288942 212288955 - ACTACTGGTATAGTGCTGGTTTGTTCA 0 AGAACGTTTGCCTCAGCCTCCCATCTG 0 - ILLUMINA NA 190 TRUE -ERBB4_3_4 ERBB4_3_4.chr2.212530066.212530135 ERBB4_3_4.chr2.212530066.212530135_tile_1 Homo sapiens hg19 chr2 212530066 212530135 - CATTTCAGGGTCCTGACAACTGTACAA 0 AACTGCACCCAAGGGTAAGCATTCTT 0 - ILLUMINA NA 176 TRUE -ERBB4_5 ERBB4_5.chr2.212576857.212576857 ERBB4_5.chr2.212576857.212576857_tile_1 Homo sapiens hg19 chr2 212576857 212576857 - ATACTCTGCTATTTTATAATGAAGATGCAA 0 CCAGTAACATTGACAAATTCATAAACTGTA 0 - ILLUMINA NA 171 TRUE -ERBB4_6_7 ERBB4_6_7.chr2.212578341.212578349 ERBB4_6_7.chr2.212578341.212578349_tile_1 Homo sapiens hg19 chr2 212578341 212578349 - AGGGTAAGATACATAAACACTATCAATGA 0 TGCCTGCCCTAGTTCCAAGATGGAA 0 - ILLUMINA NA 186 TRUE -ERBB4_8 ERBB4_8.chr2.212587147.212587147 ERBB4_8.chr2.212587147.212587147_tile_1 Homo sapiens hg19 chr2 212587147 212587147 - TGAAAGTAATATTTGCTGTGTTGCAGG 0 CATTCTGTGTCAAGAAATGTCCACGTA 0 - ILLUMINA NA 172 TRUE -ERBB4_9 ERBB4_9.chr2.212589811.212589811 ERBB4_9.chr2.212589811.212589811_tile_1 Homo sapiens hg19 chr2 212589811 212589811 - GCAGACTTTGATCATGGTCCTATCTCT 0 GACTGCTTTGTATGTCTGTGATTTCTC 0 - ILLUMINA NA 176 TRUE -ERBB4_10 ERBB4_10.chr2.212652764.212652764 ERBB4_10.chr2.212652764.212652764_tile_1 Homo sapiens hg19 chr2 212652764 212652764 - AATGGTGGAGTCTATGTAGACCAGAAC 0 TCTTTTTAATTTCTCAAAATGTTCTACCCT 0 - ILLUMINA NA 172 TRUE -ERBB4_11 ERBB4_11.chr2.212812157.212812157 ERBB4_11.chr2.212812157.212812157_tile_1 Homo sapiens hg19 chr2 212812157 212812157 - GTGGCTCTTAATCAGTTTCGTTACCTG 0 GGTAAGGAATATATCCAAAATGGCAAATA 0 - ILLUMINA NA 186 TRUE -VHL1_2 VHL1_2.chr3.10183797.10183817 VHL1_2.chr3.10183797.10183817_tile_1 Homo sapiens hg19 chr3 10183797 10183817 - AAAATGGACCCCGGGGCGGTAGAGGG 0 ATACGGGCAGCACGACGCGCGGACT 0 - ILLUMINA NA 185 TRUE -VHL3_5 VHL3_5.chr3.10188245.10188301 VHL3_5.chr3.10188245.10188301_tile_1 Homo sapiens hg19 chr3 10188245 10188301 - GAACTGGGCTTAATTTTTCAAGTGGTC 0 AGAAGCCCATCGTGTGTCCCTGCATCT 0 - ILLUMINA NA 186 TRUE -VHL6_8 VHL6_8.chr3.10191480.10191506 VHL6_8.chr3.10191480.10191506_tile_1 Homo sapiens hg19 chr3 10191480 10191506 - TTGATGTGCAATGCGCTCCTGTGTCAG 0 GTATACACTGGAAGGGCAAAAACCAAAT 0 - ILLUMINA NA 186 TRUE -MLH1 MLH1.chr3.37067240.37067240 MLH1.chr3.37067240.37067240_tile_1 Homo sapiens hg19 chr3 37067240 37067240 - TGGGAGTTCAAGCATCTCCTCATCTTG 0 ATCTGGTGGGCATAGACCTTATCACT 0 - ILLUMINA NA 184 TRUE -CTNNB1_1_16 CTNNB1_1_16.chr3.41266040.41266137 CTNNB1_1_16.chr3.41266040.41266137_tile_1 Homo sapiens hg19 chr3 41266040 41266137 - GGTATCCACATCCTCTTCCTCAGGATT 0 GTCCAACTCCATCAAATCAGCTATAAA 0 - ILLUMINA NA 172 TRUE -PIK3CA1 PIK3CA1.chr3.178916876.178916876 PIK3CA1.chr3.178916876.178916876_tile_1 Homo sapiens hg19 chr3 178916876 178916876 - AGGGACAACAGTTAAGCTTTATGGTTA 0 AAAAATTCTTCCCTTTCTGCTTCTTG 0 - ILLUMINA NA 190 TRUE -PIK3CA2 PIK3CA2.chr3.178921553.178921553 PIK3CA2.chr3.178921553.178921553_tile_1 Homo sapiens hg19 chr3 178921553 178921553 - ACATTCGGAGATTTGGATGTTCTCCTA 0 TCACGTAGGTTGCACAAAGAATTTTTA 0 - ILLUMINA NA 186 TRUE -PIK3CA3 PIK3CA3.chr3.178927980.178927980 PIK3CA3.chr3.178927980.178927980_tile_1 Homo sapiens hg19 chr3 178927980 178927980 - CTTCTAATCCATGAGGTACTGGCCAAA 0 AACACATTTCAAAACACTTTTCTTCCC 0 - ILLUMINA NA 178 TRUE -PIK3CA4_11 PIK3CA4_11.chr3.178936074.178936095 PIK3CA4_11.chr3.178936074.178936095_tile_1 Homo sapiens hg19 chr3 178936074 178936095 - GGTATGGTAAAAACATGCTGAGATCAG 0 CTCGTGTAGAAATTGCTTTGAGCTGTT 0 - ILLUMINA NA 172 TRUE -PIK3CA12 PIK3CA12.chr3.178938860.178938860 PIK3CA12.chr3.178938860.178938860_tile_1 Homo sapiens hg19 chr3 178938860 178938860 - TAAACAACTCTGCCCCACTGCAGTGAA 0 CTTCAAATACATCCCACATGCACGACA 0 - ILLUMINA NA 174 TRUE -PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_1 Homo sapiens hg19 chr3 178952007 178952150 - CCAAAGCCTCTTGCTCAGTTTTATCTAA 0 AGCCTTGTAACACATCTCCTGAAACC 0 - ILLUMINA NA 175 TRUE -PIK3CA13_20 PIK3CA13_20.chr3.178952007.178952150 PIK3CA13_20.chr3.178952007.178952150_tile_2 Homo sapiens hg19 chr3 178952007 178952150 + CATTGCATACATTCGAAAGACCCTAGC 0 AGATAACTGAGAAAATGAAAGCTCACTCTG 0 + ILLUMINA NA 187 TRUE -FGFR3_1_2 FGFR3_1_2.chr4.1803564.1803568 FGFR3_1_2.chr4.1803564.1803568_tile_1 Homo sapiens hg19 chr4 1803564 1803568 - TTGCTGCCATTCACCTCCACGTGCTTG 0 TCTGTGGGGGCAGATGACGCTCAGG 0 - ILLUMINA NA 176 TRUE -FGFR3_3_4 FGFR3_3_4.chr4.1806119.1806153 FGFR3_3_4.chr4.1806119.1806153_tile_1 Homo sapiens hg19 chr4 1806119 1806153 - GCTCAGAACCTGGTATCTACTTTCTGT 0 TAGCTGAGGATGCCTGCATACACACTG 0 - ILLUMINA NA 188 TRUE -FGFR3_5_7 FGFR3_5_7.chr4.1807862.1807890 FGFR3_5_7.chr4.1807862.1807890_tile_1 Homo sapiens hg19 chr4 1807862 1807890 - AAACAAGGCCTCAGGCGCCATCCACT 0 GCCAGCCCGAAGTCTGCGATCT 0 - ILLUMINA NA 191 TRUE -FGFR3_8 FGFR3_8.chr4.1808331.1808331 FGFR3_8.chr4.1808331.1808331_tile_1 Homo sapiens hg19 chr4 1808331 1808331 - CCGGAGGGACCCCCACCCCTGA 0 CCCCCAGCGTGAAGATCTCCCA 0 - ILLUMINA NA 171 TRUE -FGFR3_9 FGFR3_9.chr4.1808949.1808949 FGFR3_9.chr4.1808949.1808949_tile_1 Homo sapiens hg19 chr4 1808949 1808949 - AAGCTCTGTGTAGCTGTCTCTCCATCT 0 TCGTGGGCAAACACGGAGTCGTC 0 - ILLUMINA NA 186 TRUE -PDGFRA1_4 PDGFRA1_4.chr4.55141013.55141049 PDGFRA1_4.chr4.55141013.55141049_tile_1 Homo sapiens hg19 chr4 55141013 55141049 - TACCCCATGGAACTTACCAAGCACTAG 0 CTATAAATGACCAGGACAGGTAACTGG 0 - ILLUMINA NA 178 TRUE -PDGFRA5 PDGFRA5.chr4.55144146.55144146 PDGFRA5.chr4.55144146.55144146_tile_1 Homo sapiens hg19 chr4 55144146 55144146 - GTCAGCTCCATTCAAGGGACTTCTATT 0 TACAATGTTCAAATGTGGCCCCAGGT 0 - ILLUMINA NA 188 TRUE -PDGFRA6 PDGFRA6.chr4.55144547.55144547 PDGFRA6.chr4.55144547.55144547_tile_1 Homo sapiens hg19 chr4 55144547 55144547 - AACATCTCTCTTTGCACCCACCTCCGT 0 ATGATGTAAATGGGGCCTATGGGGAC 0 - ILLUMINA NA 186 TRUE -PDGFRA7_23 PDGFRA7_23.chr4.55152040.55152109 PDGFRA7_23.chr4.55152040.55152109_tile_1 Homo sapiens hg19 chr4 55152040 55152109 - AGAGATTAAAGTGAAGGAGGATGAGCC 0 TTGCGAGCAGCCAGATCACGGTGGA 0 - ILLUMINA NA 174 TRUE -KIT1 KIT1.chr4.55561764.55561764 KIT1.chr4.55561764.55561764_tile_1 Homo sapiens hg19 chr4 55561764 55561764 - GTGTTTGTTGGTGCACGTGTATTTGC 0 CCCACGCGGACTATTAAGTCTGATTTT 0 - ILLUMINA NA 179 TRUE -KIT2 KIT2.chr4.55592185.55592186 KIT2.chr4.55592185.55592186_tile_1 Homo sapiens hg19 chr4 55592185 55592186 - CAGTATGGTGTGATGCATGTATTACCA 0 CAGAAGTCTTGCCCACATCGTTGTAA 0 - ILLUMINA NA 188 TRUE -KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_1 Homo sapiens hg19 chr4 55593464 55593689 - GAGAGAACAAATAAATGGTTACCTGTAAA 0 GTGGAATCACAAACTTTGGCAGGA 0 - ILLUMINA NA 172 TRUE -KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_2 Homo sapiens hg19 chr4 55593464 55593689 + CGTAGCTGGCATGATGTGCATTATTG 0 ACCCATGTATGAAGTACAGTGGAAGG 0 + ILLUMINA NA 175 TRUE -KIT3_19 KIT3_19.chr4.55593464.55593689 KIT3_19.chr4.55593464.55593689_tile_3 Homo sapiens hg19 chr4 55593464 55593689 - GTGACATGGAAAGCCCCTGTTTCATA 0 TCTGTGGGGAGAAAGGGAAAAATAGAT 0 - ILLUMINA NA 185 TRUE -KIT20_21 KIT20_21.chr4.55594221.55594258 KIT20_21.chr4.55594221.55594258_tile_1 Homo sapiens hg19 chr4 55594221 55594258 - GCAGTTTATAATCTAGCATTGCCAAAAT 0 AGTTCAGACATGAGGGCTTCCCGTTCT 0 - ILLUMINA NA 189 TRUE -KIT22 KIT22.chr4.55595519.55595519 KIT22.chr4.55595519.55595519_tile_1 Homo sapiens hg19 chr4 55595519 55595519 - ACTATTTATGTAAATCAGTCTTACCAGGA 0 TAATGACCAGGGTGGGCCCTAAAAGC 0 - ILLUMINA NA 184 TRUE -KIT23 KIT23.chr4.55597495.55597497 KIT23.chr4.55597495.55597497_tile_1 Homo sapiens hg19 chr4 55597495 55597497 - CCACATTAGCATGATATACATACTCTCT 0 CTGGGAGAGATGAAACAAGTCATGACT 0 - ILLUMINA NA 187 TRUE -KIT24_28 KIT24_28.chr4.55599320.55599348 KIT24_28.chr4.55599320.55599348_tile_1 Homo sapiens hg19 chr4 55599320 55599348 - TGTGTGATATCCCTAGACAGGATTTAC 0 GGCTAGACCAAAATCACAAATCTTTGT 0 - ILLUMINA NA 184 TRUE -KIT29 KIT29.chr4.55602694.55602694 KIT29.chr4.55602694.55602694_tile_1 Homo sapiens hg19 chr4 55602694 55602694 - GAAGCAGGACACCAATGAAACTTCAAG 0 TGCCATCCACTTCACAGGTAGTCGA 0 - ILLUMINA NA 186 TRUE -KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_1 Homo sapiens hg19 chr4 55946114 55946257 - ATTCTCCAGCCTGACTCGGGGACCACACTG 0 CATTTGATTTTCATTTCGACAACAGAAAAA 0 - ILLUMINA NA 173 TRUE -KDR1 KDR1.chr4.55946114.55946257 KDR1.chr4.55946114.55946257_tile_2 Homo sapiens hg19 chr4 55946114 55946257 + ATGCTTCCTTTTAAACAGGAGGAGAGC 0 GGACTGGTAGCCGCTTGTCTGGTTTGA 0 + ILLUMINA NA 188 TRUE -KDR3 KDR3.chr4.55953807.55953807 KDR3.chr4.55953807.55953807_tile_1 Homo sapiens hg19 chr4 55953807 55953807 - CTGAAGCCATAACAACAGTCTTCTGTG 0 ATTCCATTATGACAACACAGCAGGAAT 0 - ILLUMINA NA 190 TRUE -KDR4 KDR4.chr4.55955111.55955127 KDR4.chr4.55955111.55955127_tile_1 Homo sapiens hg19 chr4 55955111 55955127 - TCCTTATTTAGCATCTCACCTCGTCAG 0 AGCCCAGTCAGAGACCCACGTTTT 0 - ILLUMINA NA 174 TRUE -KDR6 KDR6.chr4.55960989.55961023 KDR6.chr4.55960989.55961023_tile_1 Homo sapiens hg19 chr4 55960989 55961023 - TTTATAGACCAAAGGGGCACGATTCCG 0 TGTAGAAGAAGAGGAAGGTACTGGCTA 0 - ILLUMINA NA 172 TRUE -KDR8 KDR8.chr4.55962507.55962507 KDR8.chr4.55962507.55962507_tile_1 Homo sapiens hg19 chr4 55962507 55962507 - GGAAATGCATGTGGTCTGTAAACTAGG 0 AACACACAGTGAGCATCGAGCTCTCA 0 - ILLUMINA NA 178 TRUE -KDR9 KDR9.chr4.55972964.55972964 KDR9.chr4.55972964.55972964_tile_1 Homo sapiens hg19 chr4 55972964 55972964 - TACCATGGTAGGCTGCGTTGGAAGTTA 0 GACAAACCCATACCCTTGTGAAGAATG 0 - ILLUMINA NA 172 TRUE -KDR10 KDR10.chr4.55979623.55979623 KDR10.chr4.55979623.55979623_tile_1 Homo sapiens hg19 chr4 55979623 55979623 - CTGGTGTCCCTGTTTTTAGCATTAAAT 0 ACCTAAAAACCCAGTCTGGGAGTGAG 0 - ILLUMINA NA 182 TRUE -KDR11 KDR11.chr4.55980348.55980348 KDR11.chr4.55980348.55980348_tile_1 Homo sapiens hg19 chr4 55980348 55980348 - TCTGTGCAAAGTTATAGGCTTATTTGC 0 AGAACTGAACTAAATGTGGGGATTGAC 0 - ILLUMINA NA 178 TRUE -FBXW7_1 FBXW7_1.chr4.153245446.153245446 FBXW7_1.chr4.153245446.153245446_tile_1 Homo sapiens hg19 chr4 153245446 153245446 - CAGTAATTGATAGGAAGAGTATCCATACT 0 AACAAGTGGAATGGAACTCAAAGACAA 0 - ILLUMINA NA 190 TRUE -FBXW7_2 FBXW7_2.chr4.153247288.153247366 FBXW7_2.chr4.153247288.153247366_tile_1 Homo sapiens hg19 chr4 153247288 153247366 - GTTTTGTTTTGTTTTTCTGTTTCTCCCT 0 TATGATGGCAGGAGGGTTGTTAGTGGAGCA 0 - ILLUMINA NA 171 TRUE -FBXW7_5 FBXW7_5.chr4.153249384.153249384 FBXW7_5.chr4.153249384.153249384_tile_1 Homo sapiens hg19 chr4 153249384 153249384 - CATACAGGTGGAGTATGGTCATCACAA 0 AAAAGGTAAGGGAAAATCTTGTCATGG 0 - ILLUMINA NA 184 TRUE -FBXW7_7 FBXW7_7.chr4.153250883.153250883 FBXW7_7.chr4.153250883.153250883_tile_1 Homo sapiens hg19 chr4 153250883 153250883 - CTGTTCCTGTTTATGCCTTCATTTTTC 0 AGTTAGTGGTTCTGATGACAACACTT 0 - ILLUMINA NA 180 TRUE -FBXW7_8 FBXW7_8.chr4.153258983.153258983 FBXW7_8.chr4.153258983.153258983_tile_1 Homo sapiens hg19 chr4 153258983 153258983 - CTGTAATTTGGGACATCTGTTAAAACAATA 0 GACTTCATTTCATTGCTCCCTAAAGAGG 0 - ILLUMINA NA 191 TRUE -APC1 APC1.chr5.112173917.112173917 APC1.chr5.112173917.112173917_tile_1 Homo sapiens hg19 chr5 112173917 112173917 - GCAGAGCTTCTTCTAAGTGCATTTCTC 0 TGAAGAAGTTCCTGGATTTTCTGTTGC 0 - ILLUMINA NA 186 TRUE -APC2 APC2.chr5.112174631.112174631 APC2.chr5.112174631.112174631_tile_1 Homo sapiens hg19 chr5 112174631 112174631 - AATTTGTTGGTCTCTCTTCTTCTTCAT 0 TTTGTTTCTGAACCATTGGCTCCCCGT 0 - ILLUMINA NA 174 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_1 Homo sapiens hg19 chr5 112175162 112175958 + CTTGCAAAGTTTCTTCTATTAACCAAGA 0 TTCTGCTAATACCCTGCAAATAGCAGA 0 + ILLUMINA NA 176 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_2 Homo sapiens hg19 chr5 112175162 112175958 - TGCTGGATTTGGTTCTAGGGTGCT 0 CCTATTTCATCTTCAGCTGATGACAAA 0 - ILLUMINA NA 171 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_3 Homo sapiens hg19 chr5 112175162 112175958 + GAAAAGATTGGAACTAGGTCAGCTGAAG 0 AGCGAAATCTCCCTCCAAAAGTGGT 0 + ILLUMINA NA 172 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_4 Homo sapiens hg19 chr5 112175162 112175958 - CTATCAAGTGAACTGACAGAAGTACATC 0 CCTGGCTGATTCTGAAGATAAACTAGAACC 0 - ILLUMINA NA 171 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_5 Homo sapiens hg19 chr5 112175162 112175958 + CACCCAAAAGTCCACCTGAACACTAT 0 ATTATAAGCCCCAGTGATCTTCCAGAT 0 + ILLUMINA NA 174 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_6 Homo sapiens hg19 chr5 112175162 112175958 - CTCTCTCTTTTCAGCAGTAGGTGCTT 0 CACTTACCATTCCACTGCATGGTTCA 0 - ILLUMINA NA 173 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_7 Homo sapiens hg19 chr5 112175162 112175958 + CAAACCAAGCGAGAAGTACCTAAAAAT 0 AAAGTACTCCAGATGGATTTTCTTGTTC 0 + ILLUMINA NA 171 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_8 Homo sapiens hg19 chr5 112175162 112175958 - CTCTGATTCTGTTTCATTCCCATTGTCATT 0 GTGGCAAAATGTAATAAAGTATCAGCATCT 0 - ILLUMINA NA 173 TRUE -APC3_42 APC3_42.chr5.112175162.112175958 APC3_42.chr5.112175162.112175958_tile_9 Homo sapiens hg19 chr5 112175162 112175958 + ATTAAGAATAATGCCTCCAGTTCAGGA 0 AGAAGAATGTATTATTTCTGCCATGCC 0 + ILLUMINA NA 190 TRUE -CSF1R1_3 CSF1R1_3.chr5.149433644.149433646 CSF1R1_3.chr5.149433644.149433646_tile_1 Homo sapiens hg19 chr5 149433644 149433646 - TCCCACCCTCAGGACTATACCAATCT 0 AGTTCTGCTGAGGAGTTGACGACAGGG 0 - ILLUMINA NA 185 TRUE -CSF1R4 CSF1R4.chr5.149453044.149453044 CSF1R4.chr5.149453044.149453044_tile_1 Homo sapiens hg19 chr5 149453044 149453044 - TCTTGGGTGGTGGGGACTATGTACCT 0 AACTTGAGCTCTGAGCAGAACCTCATC 0 - ILLUMINA NA 175 TRUE -NPM1 NPM1.chr5.170837547.170837548 NPM1.chr5.170837547.170837548_tile_1 Homo sapiens hg19 chr5 170837547 170837548 - GGTAGGGAAAGTTCTCACTCTGCATTA 0 AAAAAGAAATGTGGTTAAGGAACCAC 0 - ILLUMINA NA 186 TRUE -EGFR1 EGFR1.chr7.55211080.55211080 EGFR1.chr7.55211080.55211080_tile_1 Homo sapiens hg19 chr7 55211080 55211080 - CATCGGAACTGCTGTCTGCATTTATGA 0 GATGATCTGCAGGTTTTCCAAAGGAAT 0 - ILLUMINA NA 188 TRUE -EGFR2 EGFR2.chr7.55221822.55221822 EGFR2.chr7.55221822.55221822_tile_1 Homo sapiens hg19 chr7 55221822 55221822 - AAGCAAGGCAAACACATCCACCCAAAG 0 AAAGCTGTATTTGCCCTCGGGGTTCA 0 - ILLUMINA NA 174 TRUE -EGFR3 EGFR3.chr7.55233043.55233043 EGFR3.chr7.55233043.55233043_tile_1 Homo sapiens hg19 chr7 55233043 55233043 - AACTTGGGAGACATTTTTGATCTCTGA 0 TGCCGGGCAGGTCTTGACGCAGT 0 - ILLUMINA NA 186 TRUE -EGFR4 EGFR4.chr7.55241677.55241708 EGFR4.chr7.55241677.55241708_tile_1 Homo sapiens hg19 chr7 55241677 55241708 - GGAAATATACAGCTTGCAAGGACTCTG 0 TCAAGATCCTCAAGAGAGCTTGGTTG 0 - ILLUMINA NA 180 TRUE -EGFR9 EGFR9.chr7.55242418.55242511 EGFR9.chr7.55242418.55242511_tile_1 Homo sapiens hg19 chr7 55242418 55242511 - ATGAGAAAAGGTGGGCCTGAGGTTCAG 0 CCTATGACAGAGAGAGAAGGAAGACGTT 0 - ILLUMINA NA 190 TRUE -EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_1 Homo sapiens hg19 chr7 55249005 55249131 - AGGTGAGGCAGATGCCCAGCAGGCGG 0 CGCATGAATGCGATCTTGAGTTTCAA 0 - ILLUMINA NA 175 TRUE -EGFR44 EGFR44.chr7.55249005.55249131 EGFR44.chr7.55249005.55249131_tile_2 Homo sapiens hg19 chr7 55249005 55249131 + CAGCGTGGACAACCCCCACGTGT 0 GTGTGTGCAGATCGCAAAGGTAATCA 0 + ILLUMINA NA 177 TRUE -EGFR54 EGFR54.chr7.55259514.55259524 EGFR54.chr7.55259514.55259524_tile_1 Homo sapiens hg19 chr7 55259514 55259524 - CCTCCCCTGCATGTGTTAAACAATACA 0 CCAAAATCTGTGATCTTGACATGCTGC 0 - ILLUMINA NA 178 TRUE -MET1 MET1.chr7.116339642.116339642 MET1.chr7.116339642.116339642_tile_1 Homo sapiens hg19 chr7 116339642 116339642 - CCTTCTCACTGATATCGAATGCAATGG 0 CTTCTATCTGTGGGGAGAATATGCAGT 0 - ILLUMINA NA 180 TRUE -MET2 MET2.chr7.116340262.116340262 MET2.chr7.116340262.116340262_tile_1 Homo sapiens hg19 chr7 116340262 116340262 - GCCCTGGATATTCTTTTTGAGACTGAT 0 GAAGAAGTCGTTGACATATTTGATAGG 0 - ILLUMINA NA 188 TRUE -MET3 MET3.chr7.116411990.116411990 MET3.chr7.116411990.116411990_tile_1 Homo sapiens hg19 chr7 116411990 116411990 - TGCAAAACCAAAAATAAACAACAATGTC 0 TTACACTTCGGGCACTTACAAGCCTA 0 - ILLUMINA NA 171 TRUE -MET4 MET4.chr7.116417463.116417464 MET4.chr7.116417463.116417464_tile_1 Homo sapiens hg19 chr7 116417463 116417464 - CACAAGGGGAAAGTGTAAATCAACGTTT 0 CACAACCAAAATGCCCTGTGCAAAAGA 0 - ILLUMINA NA 191 TRUE -MET6 MET6.chr7.116423413.116423474 MET6.chr7.116423413.116423474_tile_1 Homo sapiens hg19 chr7 116423413 116423474 - GAGGAGAAACTCAGAGATAACCAATAC 0 TGTCTCTGGCAAGACCAAAATCAGCA 0 - ILLUMINA NA 172 TRUE -SMO1 SMO1.chr7.128845101.128845101 SMO1.chr7.128845101.128845101_tile_1 Homo sapiens hg19 chr7 128845101 128845101 - TGACCAGGGTGAAGAGCGTGCAGAG 0 AAGGGCACTTCGCACTGGCCTGAA 0 - ILLUMINA NA 186 TRUE -SMO2 SMO2.chr7.128846040.128846040 SMO2.chr7.128846040.128846040_tile_1 Homo sapiens hg19 chr7 128846040 128846040 - ATTGCCACAGTGAGGACAAAGGGGAGT 0 GTACACGATGACAAAGATGATGACGCA 0 - ILLUMINA NA 186 TRUE -SMO3 SMO3.chr7.128846374.128846374 SMO3.chr7.128846374.128846374_tile_1 Homo sapiens hg19 chr7 128846374 128846374 - TAGCTGGGGTTTCAGCATGGGGGCAGC 0 AAGCCCGCACGGTATCGGTAGTTCT 0 - ILLUMINA NA 190 TRUE -SMO4 SMO4.chr7.128850341.128850341 SMO4.chr7.128850341.128850341_tile_1 Homo sapiens hg19 chr7 128850341 128850341 - AACCACTGACCAAGGCTGTGCTAGAGG 0 TCATGGCGATGCCAGTTCCAAACA 0 - ILLUMINA NA 190 TRUE -SMO5 SMO5.chr7.128851593.128851593 SMO5.chr7.128851593.128851593_tile_1 Homo sapiens hg19 chr7 128851593 128851593 - TTCAGATCCTCTGGGGCCTTTCCTTC 0 AGAAATATCCTGGGGCAGTATGGCTCC 0 - ILLUMINA NA 173 TRUE -BRAF1 BRAF1.chr7.140453121.140453193 BRAF1.chr7.140453121.140453193_tile_1 Homo sapiens hg19 chr7 140453121 140453193 - ACCTAAACTCTTCATAATGCTTGCTCT 0 GGTCCCATCAGTTTGAACAGTTGTCT 0 - ILLUMINA NA 176 TRUE -BRAF28 BRAF28.chr7.140481397.140481478 BRAF28.chr7.140481397.140481478_tile_1 Homo sapiens hg19 chr7 140481397 140481478 - GGTTTTCTTTTTCTGTTTGGCTTGACT 0 CTACAAGGGAAAGTGGCATGGTAAGTA 0 - ILLUMINA NA 178 TRUE -FGFR1_1 FGFR1_1.chr8.38282209.38282209 FGFR1_1.chr8.38282209.38282209_tile_1 Homo sapiens hg19 chr8 38282209 38282209 - TTTTGAGAGGCTTGGGCTCAGCAGAA 0 TCACCGGCCCATCCTGCAAGCAGGG 0 - ILLUMINA NA 179 TRUE -FGFR1_2 FGFR1_2.chr8.38285938.38285938 FGFR1_2.chr8.38285938.38285938_tile_1 Homo sapiens hg19 chr8 38285938 38285938 - AAGAGATCATCACTAAGGGAGCAGTGG 0 GGATGATGATGATGATGATGACTCCTC 0 - ILLUMINA NA 184 TRUE -JAK2_1 JAK2_1.chr9.5073769.5073770 JAK2_1.chr9.5073769.5073770_tile_1 Homo sapiens hg19 chr9 5073769 5073770 - TTCAGTTTCAAAAATACTTAACTCCTGTT 0 CTCCATAATTTAAAACCAAATGCTTGTG 0 - ILLUMINA NA 188 TRUE -CDKN2A1 CDKN2A1.chr9.21971153.21971187 CDKN2A1.chr9.21971153.21971187_tile_1 Homo sapiens hg19 chr9 21971153 21971187 - TTGTGTGGGGGTCTGCTTGGCGGTGA 0 AACTGCGCCGACCCCGCCACTCTCA 0 - ILLUMINA NA 187 TRUE -ABL1_1 ABL1_1.chr9.133738330.133738364 ABL1_1.chr9.133738330.133738364_tile_1 Homo sapiens hg19 chr9 133738330 133738364 - ATGCATCGCCTAATGCCAGCAGACGC 0 TGATGTCCGTGCGTTCCATCTCCCAC 0 - ILLUMINA NA 191 TRUE -ABL1_9 ABL1_9.chr9.133747520.133747520 ABL1_9.chr9.133747520.133747520_tile_1 Homo sapiens hg19 chr9 133747520 133747520 - AGCGCCTGTGTCACCCTGGGGGT 0 AAAACGAAGGTGAAATTATTTCAGGAA 0 - ILLUMINA NA 190 TRUE -ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_1 Homo sapiens hg19 chr9 133748283 133748414 + AGAATCCTTCAGAAGGCTTTTTCTTTAGAC 0 AACCTCCTGGACTACCTGAGGGAGT 0 + ILLUMINA NA 172 TRUE -ABL1_10 ABL1_10.chr9.133748283.133748414 ABL1_10.chr9.133748283.133748414_tile_2 Homo sapiens hg19 chr9 133748283 133748414 - TCCATGGCGCAGGCTGCCTGGCC 0 CCGTAGGTCATGAACTCAGTGATGA 0 - ILLUMINA NA 182 TRUE -ABL1_16 ABL1_16.chr9.133750356.133750356 ABL1_16.chr9.133750356.133750356_tile_1 Homo sapiens hg19 chr9 133750356 133750356 - GGGAAGAGCAAGAAAGAGGCAGAAAAA 0 TGTGTAGGTGTCCCCTGTCATCAA 0 - ILLUMINA NA 190 TRUE -NOTCH1_1 NOTCH1_1.chr9.139397768.139397768 NOTCH1_1.chr9.139397768.139397768_tile_1 Homo sapiens hg19 chr9 139397768 139397768 - AGACCTGGCTTCCCACCACCCCAGGCT 0 AGATTGACAACCGGCAGTGTGTGCAG 0 - ILLUMINA NA 190 TRUE -NOTCH1_2 NOTCH1_2.chr9.139399344.139399422 NOTCH1_2.chr9.139399344.139399422_tile_1 Homo sapiens hg19 chr9 139399344 139399422 - AGTGCGAGTGGGACGGGCTGGACTGT 0 ACACCAACGTGGTCTTCAAGCGTGAC 0 - ILLUMINA NA 171 TRUE -RET1 RET1.chr10.43609078.43609104 RET1.chr10.43609078.43609104_tile_1 Homo sapiens hg19 chr10 43609078 43609104 - ACTCGCCTCCCAGCAATTTCCTCCC 0 TTGCAGGTGCCATAGCCAGCTTTAAT 0 - ILLUMINA NA 180 TRUE -RET2_9 RET2_9.chr10.43609940.43609950 RET2_9.chr10.43609940.43609950_tile_1 Homo sapiens hg19 chr10 43609940 43609950 + AAGCCTCACACCACCCCCACCCACAGAT 0 CCCATCTCCTCAGCTGAGATGACCTT 0 + ILLUMINA NA 175 TRUE -RET10 RET10.chr10.43613840.43613840 RET10.chr10.43613840.43613840_tile_1 Homo sapiens hg19 chr10 43613840 43613840 - AGAACAGGGCTGTATGGAGCCCCCAGC 0 GGGAGGCGTTCTCTGAAATGCAG 0 - ILLUMINA NA 190 TRUE -RET11_12 RET11_12.chr10.43615567.43615569 RET11_12.chr10.43615567.43615569_tile_1 Homo sapiens hg19 chr10 43615567 43615569 - ATGGTGCACCTGGGATCCCTGGGAG 0 ATGTTTCTGGCTGCCAAGTCCCGATGAA 0 - ILLUMINA NA 172 TRUE -RET13 RET13.chr10.43617416.43617416 RET13.chr10.43617416.43617416_tile_1 Homo sapiens hg19 chr10 43617416 43617416 - AATTCCCTGGCCAAGCTGCACAGACGG 0 CCATTTAACTGGAATCCGACCCTAAAG 0 - ILLUMINA NA 178 TRUE -PTEN1 PTEN1.chr10.89624242.89624244 PTEN1.chr10.89624242.89624244_tile_1 Homo sapiens hg19 chr10 89624242 89624244 - TACGGACATTTTCGCATCCGTCTACTC 0 ATGATGGCTGTCATGTCTGGGAGCCTG 0 - ILLUMINA NA 176 TRUE -PTEN3 PTEN3.chr10.89685307.89685307 PTEN3.chr10.89685307.89685307_tile_1 Homo sapiens hg19 chr10 89685307 89685307 - TGGACTTCTTGACTTAATCGGTTTAGG 0 CTTGTAATGGTTTTTATGCTTTGAATCCA 0 - ILLUMINA NA 186 TRUE -PTEN4 PTEN4.chr10.89711893.89711900 PTEN4.chr10.89711893.89711900_tile_1 Homo sapiens hg19 chr10 89711893 89711900 - GGATGAGAATTTCAAGCACTTACTGCA 0 TGGGAATAGTTACTCCCTGGTGGACA 0 - ILLUMINA NA 176 TRUE -PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_1 Homo sapiens hg19 chr10 89717615 89717772 - GGGTCCTGAATTGGAGGAATATATCTTCAC 0 ACACGAAATATGGATTCTGTATCTGC 0 - ILLUMINA NA 181 TRUE -PTEN7 PTEN7.chr10.89717615.89717772 PTEN7.chr10.89717615.89717772_tile_2 Homo sapiens hg19 chr10 89717615 89717772 + CAGTTTGTGGTCTGCCAGCTAAA 0 AAAGGTTTGTACTTTACTTTCATTGGGAG 0 + ILLUMINA NA 188 TRUE -PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_1 Homo sapiens hg19 chr10 89720716 89720852 - AATTTGGAGAAAAGTATCGGTTGGCTT 0 AGGTTTCCTCTGGTCCTGGTATGAA 0 - ILLUMINA NA 188 TRUE -PTEN13 PTEN13.chr10.89720716.89720852 PTEN13.chr10.89720716.89720852_tile_2 Homo sapiens hg19 chr10 89720716 89720852 + AAAATGATCTTGACAAAGCAAATAAAGAC 0 CTTGCTTGACAAGTTTTTAACTTATGTATT 0 + ILLUMINA NA 179 TRUE -FGFR2_1 FGFR2_1.chr10.123258034.123258034 FGFR2_1.chr10.123258034.123258034_tile_1 Homo sapiens hg19 chr10 123258034 123258034 - CTAACAGTAGCTGCCCATGAGTTAGAG 0 TTCTTGGAGCCTGCACACAGGATGGTG 0 - ILLUMINA NA 180 TRUE -FGFR2_2 FGFR2_2.chr10.123274774.123274803 FGFR2_2.chr10.123274774.123274803_tile_1 Homo sapiens hg19 chr10 123274774 123274803 - GCCTTTTGGTTCCTTTGGTTGTGCTAT 0 CATAGGGGTCTTCTTAATCGCCTGTAT 0 - ILLUMINA NA 186 TRUE -FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_1 Homo sapiens hg19 chr10 123279503 123279677 - CACGTGGAAAAGAACGGCAGTAAATAC 0 GGAGTTGAGAGAGGATGATTCTCTTTT 0 - ILLUMINA NA 172 TRUE -FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_2 Homo sapiens hg19 chr10 123279503 123279677 + TTTAGATTCAGAAAGTCCTCACCTTGAG 0 CTCCTCCGACCACTGTGGAGGCATTT 0 + ILLUMINA NA 171 TRUE -FGFR2_5 FGFR2_5.chr10.123279503.123279677 FGFR2_5.chr10.123279503.123279677_tile_3 Homo sapiens hg19 chr10 123279503 123279677 - ACTGACAGCCCTCTGGACAACACAGCT 0 CGTAGAGTTTGTCTGCAAGGTTTACAG 0 - ILLUMINA NA 184 TRUE -HRAS1 HRAS1.chr11.533873.533875 HRAS1.chr11.533873.533875_tile_1 Homo sapiens hg19 chr11 533873 533875 - TACCAGGGAGAGGCTGGCTGTGTGAAC 0 AGTACAGCGCCATGCGGGACCAGTAC 0 - ILLUMINA NA 180 TRUE -HRAS6 HRAS6.chr11.534285.534289 HRAS6.chr11.534285.534289_tile_1 Homo sapiens hg19 chr11 534285 534289 - CTGCCCTGTGGGGCCTGGGGCTGG 0 AAGAGTGCGCTGACCATCCAGCTGATC 0 - ILLUMINA NA 185 TRUE -ATM1 ATM1.chr11.108117847.108117848 ATM1.chr11.108117847.108117848_tile_1 Homo sapiens hg19 chr11 108117847 108117848 - GAAAGGAATAGTTGCATGTACAGAGTC 0 GATATCTGCCATCAATTCAATCAAATTTT 0 - ILLUMINA NA 174 TRUE -ATM2 ATM2.chr11.108119823.108119823 ATM2.chr11.108119823.108119823_tile_1 Homo sapiens hg19 chr11 108119823 108119823 - TTGCTAGTAATAGGTTTGGGGGTAGAC 0 GATCAAAATCATTCTGTGACTTCTGAA 0 - ILLUMINA NA 172 TRUE -ATM3 ATM3.chr11.108123551.108123551 ATM3.chr11.108123551.108123551_tile_1 Homo sapiens hg19 chr11 108123551 108123551 - AAGCTATAGCTTAAAATGATAAAGAGCAT 0 ACAAAGAAAAACAAAAAGCTTCACTTAGA 0 - ILLUMINA NA 172 TRUE -ATM4 ATM4.chr11.108137973.108138003 ATM4.chr11.108137973.108138003_tile_1 Homo sapiens hg19 chr11 108137973 108138003 - ACTGCCAAATCAATATAAAGAAGTAAAAGA 0 GATTTCCATTAGTATCATCTTCCATTGAT 0 - ILLUMINA NA 189 TRUE -ATM6 ATM6.chr11.108155132.108155132 ATM6.chr11.108155132.108155132_tile_1 Homo sapiens hg19 chr11 108155132 108155132 - TCGAATAAATAGCCTTAAAACTTAAAGGTT 0 ATCCCACTGTCTCTGGTACCCTCATAG 0 - ILLUMINA NA 179 TRUE -ATM7 ATM7.chr11.108170476.108170479 ATM7.chr11.108170476.108170479_tile_1 Homo sapiens hg19 chr11 108170476 108170479 - ACTCACCAATCTTCTACCAGTGTGTTA 0 ACTTCTCCCAAGCAGCTTCCAACAGCC 0 - ILLUMINA NA 178 TRUE -ATM9 ATM9.chr11.108172421.108172421 ATM9.chr11.108172421.108172421_tile_1 Homo sapiens hg19 chr11 108172421 108172421 - ACAGAACTGTTTTAGATATGCTGGGTA 0 AATGTTTTTCAAACAGGTAACAGCTGC 0 - ILLUMINA NA 182 TRUE -ATM10 ATM10.chr11.108173640.108173640 ATM10.chr11.108173640.108173640_tile_1 Homo sapiens hg19 chr11 108173640 108173640 - CAGGTCATAAACAAGGAATTATATCAGACT 0 ATATCATCCAGGCCTTCAAAAGGG 0 - ILLUMINA NA 191 TRUE -ATM11 ATM11.chr11.108180945.108180945 ATM11.chr11.108180945.108180945_tile_1 Homo sapiens hg19 chr11 108180945 108180945 - CCCTTATTGAGACAATGCCAACATTAA 0 CTAGATAATTTAAATCCAGCCAGAAAGC 0 - ILLUMINA NA 188 TRUE -ATM12 ATM12.chr11.108200958.108200961 ATM12.chr11.108200958.108200961_tile_1 Homo sapiens hg19 chr11 108200958 108200961 - CAAAGTCGGAATACCCACATATCATGT 0 CCTTTACTGTGTATCTTGCATAGAATAAT 0 - ILLUMINA NA 172 TRUE -ATM14 ATM14.chr11.108204681.108204681 ATM14.chr11.108204681.108204681_tile_1 Homo sapiens hg19 chr11 108204681 108204681 - TAGGTTGAAACATATGAAATTTGCCAA 0 GGGACAACAACATCTTCTAAATTCTTAAG 0 - ILLUMINA NA 174 TRUE -ATM15 ATM15.chr11.108205769.108205769 ATM15.chr11.108205769.108205769_tile_1 Homo sapiens hg19 chr11 108205769 108205769 - GACAAAATCCCAAATAAAGCAGAAAGAA 0 CCTGCTAAGCGAAATTCTGCTTTAAATG 0 - ILLUMINA NA 191 TRUE -ATM16 ATM16.chr11.108206594.108206594 ATM16.chr11.108206594.108206594_tile_1 Homo sapiens hg19 chr11 108206594 108206594 - CACCCAACCAAATGGCATCTTTTATAT 0 TTGTCTCAGGTCATCACGGCCCTTCAG 0 - ILLUMINA NA 186 TRUE -ATM17 ATM17.chr11.108218089.108218089 ATM17.chr11.108218089.108218089_tile_1 Homo sapiens hg19 chr11 108218089 108218089 - CTAGGACAACTGTTTATGCTGAAAACA 0 TCTATATGTACAAGTTCTGCTGACTGC 0 - ILLUMINA NA 188 TRUE -ATM18 ATM18.chr11.108225590.108225590 ATM18.chr11.108225590.108225590_tile_1 Homo sapiens hg19 chr11 108225590 108225590 - GCTAAGTGCACAATCTCCTCCTTTCT 0 AACAGAGTTTCCTGAGAGTTTCTCATC 0 - ILLUMINA NA 191 TRUE -ATM19 ATM19.chr11.108236086.108236203 ATM19.chr11.108236086.108236203_tile_1 Homo sapiens hg19 chr11 108236086 108236203 - TGAAGATCACACCCAAGCTTTCCATC 0 TCAGCTACTTTGTTGAAACTCTGGTCA 0 - ILLUMINA NA 185 TRUE -KRAS1 KRAS1.chr12.25378562.25378562 KRAS1.chr12.25378562.25378562_tile_1 Homo sapiens hg19 chr12 25378562 25378562 - TCTTTCCCAGAGAACAAATTAAAAGAGT 0 AGACAAGACAGGTAAGTAACACTGAAA 0 - ILLUMINA NA 187 TRUE -KRAS2 KRAS2.chr12.25380275.25380283 KRAS2.chr12.25380275.25380283_tile_1 Homo sapiens hg19 chr12 25380275 25380283 - TTGTTGTTGAGTTGTATATAACACCTTTT 0 AGTACAGTGCAATGAGGGACCAGTAC 0 - ILLUMINA NA 184 TRUE -KRAS7 KRAS7.chr12.25398255.25398285 KRAS7.chr12.25398255.25398285_tile_1 Homo sapiens hg19 chr12 25398255 25398285 - GGTACTGGTGGAGTATTTGATAGTGTAT 0 GCTAATTCAGAATCATTTTGTGGACGAAT 0 - ILLUMINA NA 191 TRUE -PTPN11_1 PTPN11_1.chr12.112888163.112888211 PTPN11_1.chr12.112888163.112888211_tile_1 Homo sapiens hg19 chr12 112888163 112888211 - TACTGACCTTTCAGAGGTAGGATCTGC 0 GTGTTCTGAATCTTGATGTGGGTGAC 0 - ILLUMINA NA 190 TRUE -PTPN11_10 PTPN11_10.chr12.112926884.112926888 PTPN11_10.chr12.112926884.112926888_tile_1 Homo sapiens hg19 chr12 112926884 112926888 - CAAGAGGCCTAGCAAGAGAATGAGAAT 0 TCTGAGACCGCACCATCTGGATGGTT 0 - ILLUMINA NA 178 TRUE -HNF1A_1 HNF1A_1.chr12.121431413.121431414 HNF1A_1.chr12.121431413.121431414_tile_1 Homo sapiens hg19 chr12 121431413 121431414 - TTGCCGCAGCCCAGACCAAACCAGCA 0 TTGAAACGGTTCCTCCGCCCCTTCTT 0 - ILLUMINA NA 175 TRUE -HNF1A_3 HNF1A_3.chr12.121432070.121432070 HNF1A_3.chr12.121432070.121432070_tile_1 Homo sapiens hg19 chr12 121432070 121432070 - ACATACCACTTACCGTGGACCTTACT 0 CGGTTGGCAAACCAGTTGTAGACA 0 - ILLUMINA NA 181 TRUE -FLT3_1 FLT3_1.chr13.28592620.28592653 FLT3_1.chr13.28592620.28592653_tile_1 Homo sapiens hg19 chr13 28592620 28592653 - CACATCACAGTAAATAACACTCTGGTG 0 TTGTCAGGGGCAATGTGAGGCTGCTATT 0 - ILLUMINA NA 178 TRUE -FLT3_13 FLT3_13.chr13.28602329.28602329 FLT3_13.chr13.28602329.28602329_tile_1 Homo sapiens hg19 chr13 28602329 28602329 - ACTTGAGTTTTACATTTTTAATGCTCCT 0 TGTCAGGTAACCCACTTCCACGAAAA 0 - ILLUMINA NA 171 TRUE -FLT3_14 FLT3_14.chr13.28608244.28608341 FLT3_14.chr13.28608244.28608341_tile_1 Homo sapiens hg19 chr13 28608244 28608341 - CTATCTGCAGAACTGCCTATTCCTAAC 0 TTCCAAGAGAAAATTTAGAGTTTGGTAAG 0 - ILLUMINA NA 190 TRUE -FLT3_22 FLT3_22.chr13.28610138.28610138 FLT3_22.chr13.28610138.28610138_tile_1 Homo sapiens hg19 chr13 28610138 28610138 + CCAGGTCCAAGATGGTAATGGGTAT 0 ATACCAATACTTTGTGAAGCCAAGGTGG 0 + ILLUMINA NA 171 TRUE -RB1_1 RB1_1.chr13.48919244.48919244 RB1_1.chr13.48919244.48919244_tile_1 Homo sapiens hg19 chr13 48919244 48919244 - CCTTTCCAATTTGCTGAAGAGTGCAAA 0 CAGTAACCTTAAAAATTTGTGTTATTTCGT 0 - ILLUMINA NA 182 TRUE -RB1_2 RB1_2.chr13.48923148.48923148 RB1_2.chr13.48923148.48923148_tile_1 Homo sapiens hg19 chr13 48923148 48923148 - GCTAACAGTTAATAAGCCAAGCAGAGA 0 AAATGTGATCCAAGAAACTTTTAGCAC 0 - ILLUMINA NA 178 TRUE -RB1_3 RB1_3.chr13.48942685.48942685 RB1_3.chr13.48942685.48942685_tile_1 Homo sapiens hg19 chr13 48942685 48942685 - ACATAAAGAAACGTGAACAAATCTGAAA 0 GGTGTTCTCTGTGTTTCAAAACTAAATAA 0 - ILLUMINA NA 173 TRUE -RB1_4 RB1_4.chr13.48955538.48955550 RB1_4.chr13.48955538.48955550_tile_1 Homo sapiens hg19 chr13 48955538 48955550 - TTCCCTATATGTTCTTGAGGTAGATGT 0 AATGTTTTATCATTTCTCTTGTCAAGTTG 0 - ILLUMINA NA 182 TRUE -RB1_6 RB1_6.chr13.49027168.49027168 RB1_6.chr13.49027168.49027168_tile_1 Homo sapiens hg19 chr13 49027168 49027168 - TTTGCAGTTTGAATGGTCAACATAACA 0 TAAAGGTGAATCCTATATGAAACATGATG 0 - ILLUMINA NA 178 TRUE -RB1_7 RB1_7.chr13.49033843.49033846 RB1_7.chr13.49033843.49033846_tile_1 Homo sapiens hg19 chr13 49033843 49033846 - GAAGTGCTTGATTTTCTTACTTGGTCC 0 TAGGCTAGCCGATACACTGTGGGAATA 0 - ILLUMINA NA 178 TRUE -RB1_8 RB1_8.chr13.49037877.49037877 RB1_8.chr13.49037877.49037877_tile_1 Homo sapiens hg19 chr13 49037877 49037877 - GGAAAATTACCTACCTCCTGAACAGCA 0 AGTAGTCAGAATTTTATTACATGGTTTTGT 0 - ILLUMINA NA 172 TRUE -RB1_9 RB1_9.chr13.49039164.49039164 RB1_9.chr13.49039164.49039164_tile_1 Homo sapiens hg19 chr13 49039164 49039164 - TGTTTTGGTGGACCCATTACATTAGAT 0 CTTTGATCAAAACACGTTTGAATGTCT 0 - ILLUMINA NA 174 TRUE -AKT1 AKT1.chr14.105246455.105246455 AKT1.chr14.105246455.105246455_tile_1 Homo sapiens hg19 chr14 105246455 105246455 - TCTGACGGGTAGAGTGTGCGTGGCTC 0 GCTCCCCTCAACAACTTCTCTGTG 0 - ILLUMINA NA 173 TRUE -CDH1_1 CDH1_1.chr16.68835649.68835650 CDH1_1.chr16.68835649.68835650_tile_1 Homo sapiens hg19 chr16 68835649 68835650 - GGCGGTGGTGGTGCCCCACTGT 0 CTTTGAATCGGGTGTCGAGGGAAAAA 0 - ILLUMINA NA 171 TRUE -CDH1_2 CDH1_2.chr16.68846137.68846137 CDH1_2.chr16.68846137.68846137_tile_1 Homo sapiens hg19 chr16 68846137 68846137 - ACATTCTCTAGTCTGGAGAGAGTTTTC 0 TTGGTGTCAGTGACTGTGATCACAGCT 0 - ILLUMINA NA 176 TRUE -CDH1_3 CDH1_3.chr16.68847274.68847277 CDH1_3.chr16.68847274.68847277_tile_1 Homo sapiens hg19 chr16 68847274 68847277 - CATCTTGCCAGGTACCATACAAACCTT 0 CACTTTCAGTGTGGTGATTACGACGTT 0 - ILLUMINA NA 178 TRUE -TP53_1 TP53_1.chr17.7574003.7574021 TP53_1.chr17.7574003.7574021_tile_1 Homo sapiens hg19 chr17 7574003 7574021 - ACTAAATGCATGTTGCTTTTGTACCGT 0 AGAGCTGAATGAGGCCTTGGAACTC 0 - ILLUMINA NA 172 TRUE -TP53_3 TP53_3.chr17.7577022.7577129 TP53_3.chr17.7577022.7577129_tile_1 Homo sapiens hg19 chr17 7577022 7577129 - ATCCTGAGTAGTGGTAATCTACTGGGA 0 AGGTAAGCAAGCAGGACAAGAAGCG 0 - ILLUMINA NA 172 TRUE -TP53_17 TP53_17.chr17.7577523.7577574 TP53_17.chr17.7577523.7577574_tile_1 Homo sapiens hg19 chr17 7577523 7577574 - AAAAAGGCCTCCCCTGCTTGCCACAGG 0 ATCATCACACTGGAAGACTCCAGGTCA 0 - ILLUMINA NA 190 TRUE -TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_1 Homo sapiens hg19 chr17 7578190 7578536 - TTTGGATGACAGAAACACTTTTCGACA 0 CCTGCTGCTTATTTGACCTCCCTATAAC 0 - ILLUMINA NA 172 TRUE -TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_2 Homo sapiens hg19 chr17 7578190 7578536 + GACCCCAGTTGCAAACCAGACCTCA 0 TGAGGAATCAGAGGCCTGGGGA 0 + ILLUMINA NA 171 TRUE -TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_3 Homo sapiens hg19 chr17 7578190 7578536 - TTGTGAGGCGCTGCCCCCACCATGAG 0 GCATCTTATCCGAGTGGAAGGAAATTTG 0 - ILLUMINA NA 171 TRUE -TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_4 Homo sapiens hg19 chr17 7578190 7578536 + CGTCTCTCCAGCCCCAGCTGCTCACCAT 0 CCACAGCTGCACAGGGCAGGTCTT 0 + ILLUMINA NA 171 TRUE -TP53_31_59 TP53_31_59.chr17.7578190.7578536 TP53_31_59.chr17.7578190.7578536_tile_5 Homo sapiens hg19 chr17 7578190 7578536 - GCATGTTTGTTTCTTTGCTGCCGTCT 0 TTGATTCCACACCCCCGCCCGGC 0 - ILLUMINA NA 179 TRUE -TP53_60 TP53_60.chr17.7579358.7579403 TP53_60.chr17.7579358.7579403_tile_1 Homo sapiens hg19 chr17 7579358 7579403 - AGATGAAGCTCCCAGAATGCCAGAGG 0 TTCTTGCATTCTGGGACAGCCAAGTCT 0 - ILLUMINA NA 185 TRUE -TP53_64 TP53_64.chr17.7579882.7579882 TP53_64.chr17.7579882.7579882_tile_1 Homo sapiens hg19 chr17 7579882 7579882 - ATGGTGTTGGGGGAGGGGGTTCCTTCT 0 CCCCTCTGAGTCAGGAAACATTTTCAG 0 - ILLUMINA NA 182 TRUE -ERBB2_1 ERBB2_1.chr17.37880219.37880261 ERBB2_1.chr17.37880219.37880261_tile_1 Homo sapiens hg19 chr17 37880219 37880261 - CATATCTCCCCAAACCCCAATGAAGAG 0 CTTTGATGGCCACTGGAATTTTCACA 0 - ILLUMINA NA 172 TRUE -ERBB2_4 ERBB2_4.chr17.37880993.37881012 ERBB2_4.chr17.37880993.37881012_tile_1 Homo sapiens hg19 chr17 37880993 37881012 - ATACACCAGTTCAGCAGGTCCTGGGAG 0 TATGCTTCCTGGGGACAAGGGTAC 0 - ILLUMINA NA 190 TRUE -ERBB2_13 ERBB2_13.chr17.37881332.37881440 ERBB2_13.chr17.37881332.37881440_tile_1 Homo sapiens hg19 chr17 37881332 37881440 - TCTGCTCCTTGGTCCTTCACCTAACCT 0 ACATCCTCCAGGTAGCTCATCCCCTGG 0 - ILLUMINA NA 186 TRUE -SMAD4_1 SMAD4_1.chr18.48575169.48575170 SMAD4_1.chr18.48575169.48575170_tile_1 Homo sapiens hg19 chr18 48575169 48575170 - TACAAAAATTGAAACACTATTGAGATCCT 0 CGCATACTGACAATATTTAACATGTTTTAG 0 - ILLUMINA NA 172 TRUE -SMAD4_2 SMAD4_2.chr18.48581198.48581198 SMAD4_2.chr18.48581198.48581198_tile_1 Homo sapiens hg19 chr18 48581198 48581198 - ATGTTGGGAAAGTTGGCAGTGCTGGTA 0 CAAAGTCATGCACATATTCATCCTTCAC 0 - ILLUMINA NA 180 TRUE -SMAD4_3 SMAD4_3.chr18.48584560.48584560 SMAD4_3.chr18.48584560.48584560_tile_1 Homo sapiens hg19 chr18 48584560 48584560 - GCTGTCTAAAAATTAAGGCCCACATGG 0 TGATGCTATCTGCAACAGTCCTTCAC 0 - ILLUMINA NA 188 TRUE -SMAD4_4 SMAD4_4.chr18.48586262.48586262 SMAD4_4.chr18.48586262.48586262_tile_1 Homo sapiens hg19 chr18 48586262 48586262 - ACTCATGTCATGATGAGTATTGTACTC 0 AATGCAAGCTCATTGTGAACAGGCCCT 0 - ILLUMINA NA 184 TRUE -SMAD4_5 SMAD4_5.chr18.48591826.48591919 SMAD4_5.chr18.48591826.48591919_tile_1 Homo sapiens hg19 chr18 48591826 48591919 - CAATACCTTGCTCTCTCAATGGCTTCT 0 AGTAAGCAATGGAACACCAATACTCAG 0 - ILLUMINA NA 188 TRUE -SMAD4_11 SMAD4_11.chr18.48593405.48593405 SMAD4_11.chr18.48593405.48593405_tile_1 Homo sapiens hg19 chr18 48593405 48593405 - GCACTTGGGTAGATCTTATGAACAGCA 0 TGCCTATGTGCAACCTTAGGAAGAAA 0 - ILLUMINA NA 172 TRUE -SMAD4_12 SMAD4_12.chr18.48603032.48603094 SMAD4_12.chr18.48603032.48603094_tile_1 Homo sapiens hg19 chr18 48603032 48603094 - AAAGAATGAAAAGCATACTTACTGATAGC 0 CTGACGCAAATCAAAGACCTTTTAAGAA 0 - ILLUMINA NA 172 TRUE -SMAD4_15 SMAD4_15.chr18.48604668.48604754 SMAD4_15.chr18.48604668.48604754_tile_1 Homo sapiens hg19 chr18 48604668 48604754 - GCATGGTATGAAGTACTTCGTCTAGGA 0 AAGGTCATCAACACCAATTCCAGCAG 0 - ILLUMINA NA 172 TRUE -STK11_1 STK11_1.chr19.1207021.1207092 STK11_1.chr19.1207021.1207092_tile_1 Homo sapiens hg19 chr19 1207021 1207092 - CGCAACTTCTTCTTCTTGAGGATCTTG 0 TAGATGACCTCGGTGGAGTCGATGCGG 0 - ILLUMINA NA 178 TRUE -STK11_4 STK11_4.chr19.1220487.1220502 STK11_4.chr19.1220487.1220502_tile_1 Homo sapiens hg19 chr19 1220487 1220502 - AAAGCCGGGGAGCCCTGGCTGGTC 0 AGATTTTGAGGGTGCCACCGGTGGTG 0 - ILLUMINA NA 181 TRUE -STK11_8 STK11_8.chr19.1221264.1221319 STK11_8.chr19.1221264.1221319_tile_1 Homo sapiens hg19 chr19 1221264 1221319 + TGTACCCCTTCGAAGGGGACAACATCTA 0 GCTTTTGTGCAGAAATGTAGGGTTGG 0 + ILLUMINA NA 177 TRUE -STK11_12 STK11_12.chr19.1223059.1223125 STK11_12.chr19.1223059.1223125_tile_1 Homo sapiens hg19 chr19 1223059 1223125 - ACATCCTGGCCGAGTCAGCAGAGCC 0 ACCGGTCCTTGGTGTCTGGGCTC 0 - ILLUMINA NA 188 TRUE -JAK3_1 JAK3_1.chr19.17945696.17945696 JAK3_1.chr19.17945696.17945696_tile_1 Homo sapiens hg19 chr19 17945696 17945696 - ATCCCTGATCCCACTTTCATTCCCTCA 0 ATGCCCATCAGTGCCCTGGATCCTG 0 - ILLUMINA NA 176 TRUE -JAK3_2 JAK3_2.chr19.17948009.17948009 JAK3_2.chr19.17948009.17948009_tile_1 Homo sapiens hg19 chr19 17948009 17948009 - TAGTGCTGTGTGCACTAATGGCAGACT 0 AGCTTGATGAGCCAAGTGTCGTAC 0 - ILLUMINA NA 190 TRUE -SRC SRC.chr20.36031762.36031762 SRC.chr20.36031762.36031762_tile_1 Homo sapiens hg19 chr20 36031762 36031762 - AAAGAGGAAGGGCCTCGCCCCTGGCAAT 0 TACTGGGGCTCGGTGGACGTGAAGTAG 0 - ILLUMINA NA 191 TRUE -GNAS1 GNAS1.chr20.57484420.57484421 GNAS1.chr20.57484420.57484421_tile_1 Homo sapiens hg19 chr20 57484420 57484421 - ACAGCTGGTTATTCCAGAGGGACTGGG 0 GCGAAGCAGGTCCTGAAACAAAATTGA 0 - ILLUMINA NA 172 TRUE -SMARCB1_1 SMARCB1_1.chr22.24133967.24133990 SMARCB1_1.chr22.24133967.24133990_tile_1 Homo sapiens hg19 chr22 24133967 24133990 - GCGAGTGGTTTTGAAACAGGTTTACA 0 ACATACGGAGGTAGTTTCCCACCTAT 0 - ILLUMINA NA 189 TRUE -SMARCB1_3 SMARCB1_3.chr22.24143240.24143240 SMARCB1_3.chr22.24143240.24143240_tile_1 Homo sapiens hg19 chr22 24143240 24143240 - TTGTGGGGAGCACAAGGTCAAAGCAG 0 ATGCGGTTCCTGTTGATGGTTGTGGA 0 - ILLUMINA NA 175 TRUE -SMARCB1_4 SMARCB1_4.chr22.24145582.24145582 SMARCB1_4.chr22.24145582.24145582_tile_1 Homo sapiens hg19 chr22 24145582 24145582 - ATGTCCTGCGTGTCAGGTCCAGAATCT 0 TTCTGCCCATCGATCTCCATGTCCAG 0 - ILLUMINA NA 176 TRUE -SMARCB1_5_6 SMARCB1_5_6.chr22.24176352.24176357 SMARCB1_5_6.chr22.24176352.24176357_tile_1 Homo sapiens hg19 chr22 24176352 24176357 - ACTCCACCCCCACCCGATCCTCAGGA 0 TGTTGGCAAGACGCCTCATCCGCCTGG 0 - ILLUMINA NA 173 TRUE -GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_1 Homo sapiens hg19 chr19 3114942 3115070 + AGTGCGCGGTCCACCCCCTCCT 0 CTGCCCACCCAGCAGGACGTGCT 0 + ILLUMINA NA 182 TRUE -GNA11_4 GNA11_4.chr19.3114942.3115070 GNA11_4.chr19.3114942.3115070_tile_2 Homo sapiens hg19 chr19 3114942 3115070 - CGGCACACCGGGCAAATGAGCC 0 TAGCCCAAGGTGGCGATGCGGTC 0 - ILLUMINA NA 177 TRUE -GNA11_5 GNA11_5.chr19.3118922.3119051 GNA11_5.chr19.3118922.3119051_tile_1 Homo sapiens hg19 chr19 3118922 3119051 + TCCTGCTCCAGCCGATGTCAGTCT 0 GATCCACTGCTTTGAGAACGTGACAT 0 + ILLUMINA NA 189 TRUE -GNA11_6 GNA11_6.chr19.3119204.3119357 GNA11_6.chr19.3119204.3119357_tile_2 Homo sapiens hg19 chr19 3119204 3119357 + GGATGGAGGAGAGCAAAGCCCTGTT 0 CATGGGGAGGGGCTCGCGGGCA 0 + ILLUMINA NA 189 TRUE -GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_1 Homo sapiens hg19 chr19 3120987 3121177 - AACATCTTCAGGATGAACTCCCGCGCC 0 ACGGCCCACCCAGCTCGACCCCC 0 - ILLUMINA NA 172 TRUE -GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_2 Homo sapiens hg19 chr19 3120987 3121177 + AGGTCCCCAGCGGGACGCCCAG 0 CAGCTCAACCTCAAGGAGTACAACCT 0 + ILLUMINA NA 187 TRUE -GNA11_7 GNA11_7.chr19.3120987.3121177 GNA11_7.chr19.3120987.3121177_tile_3 Homo sapiens hg19 chr19 3120987 3121177 - AAAAATCTCCTCCCGCGGGCAGAG 0 AGGATGGTGTCCTTCACGGCCGC 0 - ILLUMINA NA 185 TRUE -GNAQ_4 GNAQ_4.chr9.80412436.80412564 GNAQ_4.chr9.80412436.80412564_tile_1 Homo sapiens hg19 chr9 80412436 80412564 - CATTCTCATTGTGTCTTCCCTCCTCTA 0 GTAACTGAGTCCATGAAACCTATTTCC 0 - ILLUMINA NA 188 TRUE -GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_1 Homo sapiens hg19 chr9 80409379 80409508 - GCTTAGTGAATATGATCAAGTTCTCGTGG 0 GCTTTCTTGAAATTTGATTTTAGGACTTTT 0 - ILLUMINA NA 174 TRUE -GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_2 Homo sapiens hg19 chr9 80409379 80409508 + AGATAATAAAATGATAATCCATTGCCTGTC 0 TTGGCCCCCTACATCGACCATTCT 0 + ILLUMINA NA 177 TRUE -GNAQ_5 GNAQ_5.chr9.80409379.80409508 GNAQ_5.chr9.80409379.80409508_tile_3 Homo sapiens hg19 chr9 80409379 80409508 - ATTGAATTGACTTGGATGATCATCGTC 0 GGTCAGAGAGAAGAAAATGGATACACT 0 - ILLUMINA NA 182 TRUE -GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_1 Homo sapiens hg19 chr9 80343430 80343583 - GAAAATCATGTATTCCCATCTAGTCGACT 0 TTGCCCTGTGCAGCCTGCGTGTTGA 0 - ILLUMINA NA 172 TRUE -GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_2 Homo sapiens hg19 chr9 80343430 80343583 + TTCACAGCTACTGAGCTGTGGTATGA 0 AGGGGTATGTGATAATTGTTCTAAAGAGAG 0 + ILLUMINA NA 171 TRUE -GNAQ_6 GNAQ_6.chr9.80343430.80343583 GNAQ_6.chr9.80343430.80343583_tile_3 Homo sapiens hg19 chr9 80343430 80343583 - GGTCGTATACAAAAGATGGGTTGGACTTAT 0 GTTCCAGAACTCCTCGGTTATTCTGTT 0 - ILLUMINA NA 187 TRUE -GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_1 Homo sapiens hg19 chr9 80336240 80336429 - ACCATCCTCCAGTTGAACCTGAAGG 0 TTTATTGCCGTCCTGGACTCTGTGTGAGCG 0 - ILLUMINA NA 172 TRUE -GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_2 Homo sapiens hg19 chr9 80336240 80336429 + CAGGGAAGGGCAGGGCGGGTGTCTA 0 ATAATTTTGTCACTGTCTGGGTTCAGG 0 + ILLUMINA NA 172 TRUE -GNAQ_7 GNAQ_7.chr9.80336240.80336429 GNAQ_7.chr9.80336240.80336429_tile_3 Homo sapiens hg19 chr9 80336240 80336429 - CCAATGATGATTGAATACATTAGCAGAT 0 TACTCCCACTTCACGTGCGCCACAGAC 0 - ILLUMINA NA 177 TRUE -[Targets] -TargetA TargetB Target Number Chromosome Start Position End Position Probe Strand Sequence Species Build ID -MPL1_2.chr1.43815008.43815009_tile_1 MPL1_2.chr1.43815008.43815009_tile_1 1 chr1 43814982 43815163 + GGTGGCAGTTTCCTGCACACTACAGGTACCGCCCCCGCCAGGCAGGAGACTGGCGGTGGACCAGGTGGAGCCGAAGGCCTGTAAACAGGCATTCTTGGTTCGCTCTGTGACCCCAGATCTCCGTCCACCGCC Homo sapiens hg19 -NRAS1_7.chr1.115256528.115256531_tile_1 NRAS1_7.chr1.115256528.115256531_tile_1 1 chr1 115256500 115256680 + TCTTGTCCAGCTGTATCCAGTATGTCCAACAAACAGGTTTCACCATCTATAACCACTTGTTTTCTGTAAGAATCCTGGGGGTGTGGAGGGTAAGGGGGCAGGGAGGGAGGGAAGTTCAATTTTTATTA Homo sapiens hg19 -NRAS8_13.chr1.115258730.115258748_tile_1 NRAS8_13.chr1.115258730.115258748_tile_1 1 chr1 115258702 115258884 + TGCGCTTTTCCCAACACCACCTGCTCCAACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGAGCCACATCTACAGTACTTTAAAG Homo sapiens hg19 -ALK1.chr2.29432664.29432664_tile_1 ALK1.chr2.29432664.29432664_tile_1 1 chr2 29432636 29432822 + TCGGGCCATCCCGAAGTCTCCAATCTTGGCCACTCTTCCAGGGCCTGGACAGGTCAAGAGGCAGTTTCTGGCAGCAATGTCTCTGGGAAGAAAGGAAATGCATTTCCTAATTTTATCCCTAGGAAGATGAGTG Homo sapiens hg19 -ALK2.chr2.29443695.29443695_tile_1 ALK2.chr2.29443695.29443695_tile_1 1 chr2 29443667 29443836 + GTTGAATTTGCTGCAGAGCAGAGAGGGATGTAACCAAAATTAACTGAGCTGAGTCTGGGCAAATCTTAAACTGGGAGGAACAGGATACAAAGTTACATTTTCAGCAGCTACAATGTATA Homo sapiens hg19 -IDH1_1_2.chr2.209113112.209113113_tile_1 IDH1_1_2.chr2.209113112.209113113_tile_1 1 chr2 209113084 209113264 + ACGACCTATGATGATAGGTTTTACCCATCCACTCACAAGCCGGGGGATATTTTTGCAGATAATGGCTTCTCTGAAGACCGTGCCACCCAGAATATTTCGTATGGTGCCATTTGGTGATTTCCACATT Homo sapiens hg19 -ERBB4_1_2.chr2.212288942.212288955_tile_1 ERBB4_1_2.chr2.212288942.212288955_tile_1 1 chr2 212288912 212289100 + CCTTTCTCTAATAAATCAGGGATTTCTCGCGTTGGAATTCCATCATAGGGTTTTCCTCCAAAGGTCATCAGTTCCCATATAGTAACTCCTATATTGGAGAAAAAATTCTTACTTAAGCATATTAACAACATATGT Homo sapiens hg19 -ERBB4_3_4.chr2.212530066.212530135_tile_1 ERBB4_3_4.chr2.212530066.212530135_tile_1 1 chr2 212530036 212530210 + TGGATGGCATGGGTGGCACTCCCGATCTGGATCAGCATACTTGAAAATGAAACTGTTTGCCCCCTGTAAGCCATCTGGACATTTTTCCACACAGTTTGGGCCATCTTTAAAATGAGAGCACT Homo sapiens hg19 -ERBB4_5.chr2.212576857.212576857_tile_1 ERBB4_5.chr2.212576857.212576857_tile_1 1 chr2 212576821 212576990 + AATCCACAGTCTGAGCTGACATCAATGATCCTGTGCCAATGCCATCACAAGCTGTAGAAACAAGACTCAGAGTTAGGGGATTGAGAAACTTATTTTTGGCCAATAAATCA Homo sapiens hg19 -ERBB4_6_7.chr2.212578341.212578349_tile_1 ERBB4_6_7.chr2.212578341.212578349_tile_1 1 chr2 212578315 212578499 + CGCACACAAGAACTGGAATCTACCACAAAGTTATCTGATTAAAAAAAAAAAAAAGGTAAAATAAGCATTAATGTTAACATTCAGCAAACAAGCTCAAAACAAGATATTTTAGGGTTTAAAAATGATTAGCA Homo sapiens hg19 -ERBB4_8.chr2.212587147.212587147_tile_1 ERBB4_8.chr2.212587147.212587147_tile_1 1 chr2 212587115 212587285 + CTCCATATGTGTACTTTGCATTGAAATTGTGCTCCAGTTGAAAGGTGGTTGGATTGTAGACAAAGGTTTGGGGACACTGAGTAACACATGCTCCACTGTCATTGAAATTCATGCAGG Homo sapiens hg19 -ERBB4_9.chr2.212589811.212589811_tile_1 ERBB4_9.chr2.212589811.212589811_tile_1 1 chr2 212589783 212589957 + TGTGTCCTTAGGTCCTGAGCAGCCTCCAGCACATTCTCGATGGCAGCAGTCACTGACGTAAGGTCCGTAGCATCTGCCGTCACATTGTTCTGCACACACCGTCCTTGTCACTGCAGAAGAC Homo sapiens hg19 -ERBB4_10.chr2.212652764.212652764_tile_1 ERBB4_10.chr2.212652764.212652764_tile_1 1 chr2 212652706 212652876 + ATAATTCTACTTACATCCTGAACTACCATTTGTTGACACAAGAGTCAAGTTGGAAGGCCATGGGTTCCGAACAATATCTTGCCAATGAATGGTGTCTGCATAACAAAGGAATTT Homo sapiens hg19 -ERBB4_11.chr2.212812157.212812157_tile_1 ERBB4_11.chr2.212812157.212812157_tile_1 1 chr2 212812127 212812311 + TGTCAAGTTCTTTAATCCAAGTTCTTGAAGTCCAAAGTTTCCATCTTTTCTGTAGTTTAAAAATATTGCCAAGGCATATCGATCCTCATAAAGTTTTGTCCCACGAATAATGCGTAAATTCTCCAGAGG Homo sapiens hg19 -VHL1_2.chr3.10183797.10183817_tile_1 VHL1_2.chr3.10183797.10183817_tile_1 1 chr3 10183769 10183952 + GGCTCAACTTCGACGGCGAGCCGCAGCCCTACCCAACGCTGCCGCCTGGCACGGGCCGCCGCATCCACAGCTACCGAGGTACGGGCCCGGCGCTTAGGCCCGACCCAGCAGGGACGATAGCACGGTCTGAAGC Homo sapiens hg19 -VHL3_5.chr3.10188245.10188301_tile_1 VHL3_5.chr3.10188245.10188301_tile_1 1 chr3 10188217 10188401 + GGTTAACCAAACTGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATTTTTGCCAATATCACACTGCCAGGTACTGACGTTTTACTTTTTAAAAAGATAAGGTTGTTGTGGTAAGTACAGGATA Homo sapiens hg19 -VHL6_8.chr3.10191480.10191506_tile_1 VHL6_8.chr3.10191480.10191506_tile_1 1 chr3 10191450 10191634 + TCTGAAAGAGCGATGCCTCCAGGTTGTCCGGAGCCTAGTCAAGCCTGAGAATTACAGGAGACTGGACATCGTCAGGTCGCTCTACGAAGATCTGGAAGACCACCCAAATGTGCAGAAAGACCTGGAGCGG Homo sapiens hg19 -MLH1.chr3.37067240.37067240_tile_1 MLH1.chr3.37067240.37067240_tile_1 1 chr3 37067212 37067394 + GGTTCGTACAGATTCCCGGGAACAGAAGCTTGATGCATTTCTGCAGCCTCTGAGCAAACCCCTGTCCAGTCAGCCCCAGGCCATTGTCACAGAGGATAAGACAGATATTTCTAGTGGCAGGGCTAGGCAG Homo sapiens hg19 -CTNNB1_1_16.chr3.41266040.41266137_tile_1 CTNNB1_1_16.chr3.41266040.41266137_tile_1 1 chr3 41266010 41266180 + ATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGC Homo sapiens hg19 -PIK3CA1.chr3.178916876.178916876_tile_1 PIK3CA1.chr3.178916876.178916876_tile_1 1 chr3 178916836 178917024 + TGATGAAACAAGACGACTTTGTGACCTTCGGCTTTTTCAACCCTTTTTAAAAGTAATTGAACCAGTAGGCAACCGTGAAGAAAAGATCCTCAATCGAGAAATTGGTATGATACAATATCCTATTCTAAAATGCAAA Homo sapiens hg19 -PIK3CA2.chr3.178921553.178921553_tile_1 PIK3CA2.chr3.178921553.178921553_tile_1 1 chr3 178921525 178921709 + ATGTAAATATTCGAGACATTGATAAGGTAAAGTCAAATGCTGATGCTTATTATTTTATAGAAATTATTTTAGATAACCTTTTTCTTGCACTATACAGTAATCTGTTGACCTGTAGTATGTTTTCAGATGGT Homo sapiens hg19 -PIK3CA3.chr3.178927980.178927980_tile_1 PIK3CA3.chr3.178927980.178927980_tile_1 1 chr3 178927906 178928082 + TTATAATTTAGACTAGTGAATATTTTTCTTTGTTTTTTAAGGAACACTGTCCATTGGCATGGGGAAATATAAACTTGTTTGATTACACAGACACTCTAGTATCTGGAAAAATGGCTTTGAATC Homo sapiens hg19 -PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 1 chr3 178936044 178936214 + ATCCTCTCTCTGAAATCACTGAGCAGGAGAAAGATTTTCTATGGAGTCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGAATTTGG Homo sapiens hg19 -PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 1 chr3 178938832 178939004 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTCTCAAACAGGAGAAGAAGGATGAAACACAAAAGGTGTGTGACTCTAGTTTGTGTTTGAGACTCTT Homo sapiens hg19 -PIK3CA13_20.chr3.178952007.178952150_tile_1 PIK3CA13_20.chr3.178952007.178952150_tile_1 1 chr3 178951881 178952054 + TATCTAGCTATTCGACAGCATGCCAATCTCTTCATAAATCTTTTCTCAATGATGCTTGGCTCTGGAATGCCAGAACTACAATCTTTTGATGACATTGCATACATTCGAAAGACCCTAGCC Homo sapiens hg19 -PIK3CA13_20.chr3.178952007.178952150_tile_2 PIK3CA13_20.chr3.178952007.178952150_tile_2 1 chr3 178951999 178952184 - TTTCAGTTCAATGCATGCTGTTTAATTGTGTGGAAGATCCAATCCATTTTTGTTGTCCAGCCACCATGATGTGCATCATTCATTTGTTTCATGAAATACTCCAAAGCCTCTTGCTCAGTTTTATCTAAG Homo sapiens hg19 -FGFR3_1_2.chr4.1803564.1803568_tile_1 FGFR3_1_2.chr4.1803564.1803568_tile_1 1 chr4 1803538 1803712 + GCGCTCCCCGCACCGGCCCATCCTGCAGGCGGGGCTGCCGGCCAACCAGACGGCGGTGCTGGGCAGCGACGTGGAGTTCCACTGCAAGGTGTACAGTGACGCACAGCCCCACATCCAGTGGCT Homo sapiens hg19 -FGFR3_3_4.chr4.1806119.1806153_tile_1 FGFR3_3_4.chr4.1806119.1806153_tile_1 1 chr4 1806091 1806277 + CGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTA Homo sapiens hg19 -FGFR3_5_7.chr4.1807862.1807890_tile_1 FGFR3_5_7.chr4.1807862.1807890_tile_1 1 chr4 1807836 1808025 + CCGGGACGTGCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGGGCCGGCTGCCCGTGA Homo sapiens hg19 -FGFR3_8.chr4.1808331.1808331_tile_1 FGFR3_8.chr4.1808331.1808331_tile_1 1 chr4 1808295 1808464 + GCTCCCCGTACCCCGGCATCCCTGTGGAGGAGCTCTTCAAGCTGCTGAAGGAGGGCCACCGCATGGACAAGCCCGCCAACTGCACACACGACCTGTGAGTGGCATCCCTGGCCCTCCACTGGGTCC Homo sapiens hg19 -FGFR3_9.chr4.1808949.1808949_tile_1 FGFR3_9.chr4.1808949.1808949_tile_1 1 chr4 1808921 1809105 + CCTGCTGCCCCCGGCCCCACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAATGTGAGGGGTCCCTAGCAGCCCACCCTGCTGCTGGTGCACAGCCACTCCCCGGCATGAGACTCAGTGC Homo sapiens hg19 -PDGFRA1_4.chr4.55141013.55141049_tile_1 PDGFRA1_4.chr4.55141013.55141049_tile_1 1 chr4 55140981 55141157 + AAACCGAGGTATGAAATTCGCTGGAGGGTCATTGAATCAATCAGCCCAGATGGACATGAATATATTTATGTGGACCCGATGCAGCTGCCTTATGACTCAAGATGGGAGTTTCCAAGAGATGGA Homo sapiens hg19 -PDGFRA5.chr4.55144146.55144146_tile_1 PDGFRA5.chr4.55144146.55144146_tile_1 1 chr4 55144120 55144306 + AACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGG Homo sapiens hg19 -PDGFRA6.chr4.55144547.55144547_tile_1 PDGFRA6.chr4.55144547.55144547_tile_1 1 chr4 55144519 55144703 + CACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATGAAAGCAC Homo sapiens hg19 -PDGFRA7_23.chr4.55152040.55152109_tile_1 PDGFRA7_23.chr4.55152040.55152109_tile_1 1 chr4 55152012 55152184 + CGTCCTCCTGGCACAAGGAAAAATTGTGAAGATCTGTGACTTTGGCCTGGCCAGAGACATCATGCATGATTCGAACTATGTGTCGAAAGGCAGTGTACGTCCTCACTTCCCTCACTGGTCA Homo sapiens hg19 -KIT1.chr4.55561764.55561764_tile_1 KIT1.chr4.55561764.55561764_tile_1 1 chr4 55561736 55561913 + CGACGAGATTAGGCTGTTATGCACTGATCCGGGCTTTGTCAAATGGACTTTTGAGATCCTGGATGAAACGAATGAGAATAAGCAGAATGAATGGATCACGGAAAAGGCAGAAGCCACCAACACCG Homo sapiens hg19 -KIT2.chr4.55592185.55592186_tile_1 KIT2.chr4.55592185.55592186_tile_1 1 chr4 55592155 55592341 + CCTATTTTAACTTTGCATTTAAAGGTAACAACAAAGGTATATTTCTTTTTAATCCAATTTAAGGGGATGTTTAGGCTCTGTCTACCATATCAGTCATGATTTTAAGTTCATTCCAACATTGACCATGTCATTTC Homo sapiens hg19 -KIT3_19.chr4.55593464.55593689_tile_1 KIT3_19.chr4.55593464.55593689_tile_1 1 chr4 55593342 55593512 + ATTTCTCTTCCATTGTAGAGCAAATCCATCCCCACACCCTGTTCACTCCTTTGCTGATTGGTTTCGTAATCGTAGCTGGCATGATGTGCATTATTGTGATGATTCTGACCTACAAATA Homo sapiens hg19 -KIT3_19.chr4.55593464.55593689_tile_2 KIT3_19.chr4.55593464.55593689_tile_2 1 chr4 55593436 55593609 - TTCTGTGGGGAGAAAGGGAAAAATAGATCACCTTTTAATAATTATTGTCTCAGTCATTAGAGCACTCTGGAGAGAGAACAAATAAATGGTTACCTGTAAATATTTGTAGGTCAGAATCATCA Homo sapiens hg19 -KIT3_19.chr4.55593464.55593689_tile_3 KIT3_19.chr4.55593464.55593689_tile_3 1 chr4 55593556 55593739 + AACCCATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTCAG Homo sapiens hg19 -KIT20_21.chr4.55594221.55594258_tile_1 KIT20_21.chr4.55594221.55594258_tile_1 1 chr4 55594193 55594380 + CAAAGTCCTGAGTTACCTTGGTAATCACATGAATATTGTGAATCTACTTGGAGCCTGCACCATTGGAGGTAAAGCCGTGTCCAAGCTGCCTTTTATTGTCTGTCAGGTTATCAAAACATGACATTTTAATATG Homo sapiens hg19 -KIT22.chr4.55595519.55595519_tile_1 KIT22.chr4.55595519.55595519_tile_1 1 chr4 55595493 55595675 + CAGAATATTGTTGCTATGGTGATCTTTTGAATTTTTTGAGAAGAAAACGTGATTCATTTATTTGTTCAAAGCAGGAAGATCATGCAGAAGCTGCACTTTATAAGAATCTTCTGCATTCAAAGGAGTCT Homo sapiens hg19 -KIT23.chr4.55597495.55597497_tile_1 KIT23.chr4.55597495.55597497_tile_1 1 chr4 55597467 55597652 + CAGCGATAGTACTAATGAGTACATGGACATGAAACCTGGAGTTTCTTATGTTGTCCCAACCAAGGCCGACAAAAGGAGATCTGTGAGAATAGGTGAGTACCTACCTATCAAGCAACCAAGAGTAACTTTAC Homo sapiens hg19 -KIT24_28.chr4.55599320.55599348_tile_1 KIT24_28.chr4.55599320.55599348_tile_1 1 chr4 55599290 55599472 + AGAGACATCAAGAATGATTCTAATTATGTGGTTAAAGGAAACGTGAGTACCCATTCTCTGCTTGACAGTCCTGCAAAGGATTTTTAGTTTCAACTTTCGATAAAAATTGTTTCCTGTGATTTTCATAAT Homo sapiens hg19 -KIT29.chr4.55602694.55602694_tile_1 KIT29.chr4.55602694.55602694_tile_1 1 chr4 55602666 55602850 + CCTGAAAGCATTTTCAACTGTGTATACACGTTTGAAAGTGACGTCTGGTCCTATGGGATTTTTCTTTGGGAGCTGTTCTCTTTAGGTAAAATGATCCTTGCCAAAGACAACTTCATTAGACTCAGAGCATCTT Homo sapiens hg19 -KDR1.chr4.55946114.55946257_tile_1 KDR1.chr4.55946114.55946257_tile_1 1 chr4 55945984 55946155 + CGGCTACTTCCTGCTGGTGGAAAGAACAACACTTGAAAATCTGAGCAGCACCTCTCATGTGATGTCCAGGAGTTGGGGGTGTGGATGCTTCCTTTTAAACAGGAGGAGAGCT Homo sapiens hg19 -KDR1.chr4.55946114.55946257_tile_2 KDR1.chr4.55946114.55946257_tile_2 1 chr4 55946098 55946284 - GGATATCACTCCGATGACACAGACACCACCGTGTACTCCAGTGAGGAAGCAGAACTTTTAAAGCTGATAGAGATTGGAGTGCAAACCGGTAGCACAGCCCAGATTCTCCAGCCTGACTCGGGGACCACACTGA Homo sapiens hg19 -KDR3.chr4.55953807.55953807_tile_1 KDR3.chr4.55953807.55953807_tile_1 1 chr4 55953777 55953965 + TTGGGGTCACATACTTCCTCCTCCTCCATACAGGAAACAGGTGAGGTAGGCAGAGAGAGTCCAGAATCCTCTTCCATGCTCAAAGTCTCTGATATCGGAAGAACAATGTAGTCTTTGCCATCCTGAAACAATAAA Homo sapiens hg19 -KDR4.chr4.55955111.55955127_tile_1 KDR4.chr4.55955111.55955127_tile_1 1 chr4 55955085 55955257 + CCCCGTGCCAGCAGTCCAGCATGGTCTGGTACCTAGAGAAGCAAAACACTGATTTCATTAAATGCCTCTTTCTTCCTGAATGCTGAAAATAAGCACTTAAATGAGTACACATTTGTAAAGAG Homo sapiens hg19 -KDR6.chr4.55960989.55961023_tile_1 KDR6.chr4.55960989.55961023_tile_1 1 chr4 55960959 55961129 + TCACTGAGGGACTTCTCCTCCACAAATCCAGAGCTGGCTGAGCTCTGGCTACTGGTGATGCTGTCCAAGCGCCGTTTCAGATCCACAGGGATTGCTCCAACGTAGTCTTTCCCTTGA Homo sapiens hg19 -KDR8.chr4.55962507.55962507_tile_1 KDR8.chr4.55962507.55962507_tile_1 1 chr4 55962477 55962653 + GCTCCTTCTACAAATACAGTACAAAGAGGGAAATCATAGGTATGGACATTTCCTTCAATAATTGGGGTCCCTCCCTCCCTGCATGCCACTATACAACTTACCCTCCGGGGTAACACAGCTGTGA Homo sapiens hg19 -KDR9.chr4.55972964.55972964_tile_1 KDR9.chr4.55972964.55972964_tile_1 1 chr4 55972936 55973106 + ACTGAGACAGCTTGGCTATAAGAAAGAGATAACAGCGCATATTATGATTTAATTTTTCTTTAATTAGAGTCAAGAGTAAGGAAAAGATTCAGACTTTGGTTATTCTGTTCTTAGAAA Homo sapiens hg19 -KDR10.chr4.55979623.55979623_tile_1 KDR10.chr4.55979623.55979623_tile_1 1 chr4 55979595 55979775 + CTCGGTTTACAAGTTTCTTATGCTGATGCTGAAAAAAAGAGTTGACTGAACTTCCAAAGCACAGCATATAACATTACCCAATAACTTCTAGTAACACACAGAATTAAATCTGGGCTTTGGTAAACATT Homo sapiens hg19 -KDR11.chr4.55980348.55980348_tile_1 KDR11.chr4.55980348.55980348_tile_1 1 chr4 55980320 55980496 + TGCTGTACAATTTAAGACAAGCTTTTCTCCAACAGATAGTTCAATTCCATGAGACGGACTCAGAACCACATCATAAATCCTATACCCTAGAGCAAGTAAATTGAAAAAACAGAACATGAGAGA Homo sapiens hg19 -FBXW7_1.chr4.153245446.153245446_tile_1 FBXW7_1.chr4.153245446.153245446_tile_1 1 chr4 153245416 153245604 + AACGACTGGTGCCCTGTTAACGTGTGAATGCAATTCCCTGTCTCCACATCCCAAACACGGATTGATGTATCAAGAGATCCACTCACCACATGGATACCATCAAACTACAAAAGACACAGTTTATTAGAATAGA Homo sapiens hg19 -FBXW7_2.chr4.153247288.153247366_tile_1 FBXW7_2.chr4.153247288.153247366_tile_1 1 chr4 153247248 153247417 + TTGAACACAGCGGACTGCTGCAACATGACCCATCAAAACATGTAAACACTGGCCTGTCTCAATATCCCAAACCCTAAGAGTGGCATCTCGAGAACCGCTAACAACTCTGCAG Homo sapiens hg19 -FBXW7_5.chr4.153249384.153249384_tile_1 FBXW7_5.chr4.153249384.153249384_tile_1 1 chr4 153249338 153249520 + TTCATGAAGATGCATACAACGCACAGTGGAAGTATGCCCATATAAGGTGTGTATACATTCTCCAGTCTCTGCATTCCACACTTTGAGTGTCCGATCTGTAGATCCACTAATGATGATGTTGTCTCTCAT Homo sapiens hg19 -FBXW7_7.chr4.153250883.153250883_tile_1 FBXW7_7.chr4.153250883.153250883_tile_1 1 chr4 153250853 153251031 + ATTCGGTTACCACAAAACTGTAAGCATGTGATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGA Homo sapiens hg19 -FBXW7_8.chr4.153258983.153258983_tile_1 FBXW7_8.chr4.153258983.153258983_tile_1 1 chr4 153258953 153259142 + TCGTTGAAACTGGGGTTCTATCACTTGCATCATATGTTTTACTTGTGTTGGTTCACAACTATCAATGAGTTCATCTAAAGCAAGCAATTTCTCTGGTCCACTCCAGCTCTATCAAAGAGAATTAGAAATTTT Homo sapiens hg19 -APC1.chr5.112173917.112173917_tile_1 APC1.chr5.112173917.112173917_tile_1 1 chr5 112173887 112174071 + AAGCGAGGTTTGCAGATCTCCACCACTGCAGCCCAGATTGCCAAAGTCATGGAAGAAGTGTCAGCCATTCATACCTCTCAGGAAGACAGAAGTTCTGGGTCTACCACTGAATTACATTGTGTGACAGATGA Homo sapiens hg19 -APC2.chr5.112174631.112174631_tile_1 APC2.chr5.112174631.112174631_tile_1 1 chr5 112174603 112174775 + TCGAGTGGGTTCTAATCATGGAATTAATCAAAATGTAAGCCAGTCTTTGTGTCAAGAAGATGACTATGAAGATGATAAGCCTACCAATTATAGTGAACGTTACTCTGAAGAAGAACAGC Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_1 APC3_42.chr5.112175162.112175958_tile_1 1 chr5 112175034 112175208 - TCTGCTTCCTGTGTCGTCTGATTACATCCTATTTCATCTTCAGCTGATGACAAAGATGATAATGAACTACATCTTGAAAAACATATTGGAGTATCTTCTACACAATAAGTCTGTATTGTT Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_2 APC3_42.chr5.112175162.112175958_tile_2 1 chr5 112175128 112175297 + ATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCAC Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_3 APC3_42.chr5.112175162.112175958_tile_3 1 chr5 112175216 112175386 - CCTGAAGAAAATTCAACAGCTTTGTGCCTGGCTGATTCTGAAGATAAACTAGAACCCTGCAGTCTGCTGGATTTGGTTCTAGGGTGCTGTGACACTGCTGGAACTTCGCTCACAGGAT Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_4 APC3_42.chr5.112175162.112175958_tile_4 1 chr5 112175306 112175475 + CACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCA Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_5 APC3_42.chr5.112175162.112175958_tile_5 1 chr5 112175394 112175566 - GCCACTTACCATTCCACTGCATGGTTCACTCTGAACGGAGCTGGCAATCGAACGACTCTCAAAACTATCAAGTGAACTGACAGAAGTACATCTGCTAAACATGAGTGGGGTCTCCTGAAC Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_6 APC3_42.chr5.112175162.112175958_tile_6 1 chr5 112175512 112175683 + GCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATA Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_7 APC3_42.chr5.112175162.112175958_tile_7 1 chr5 112175630 112175799 - CCGTGGCAAAATGTAATAAAGTATCAGCATCTGGAAGAACCTGGACCCTCTGAACTGCAGCATTTACTGCAGCTTGCTTAGGTCCACTCTCTCTCTTTTCAGCAGTAGGTGCTTT Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_8 APC3_42.chr5.112175162.112175958_tile_8 1 chr5 112175740 112175911 + GGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAA Homo sapiens hg19 -APC3_42.chr5.112175162.112175958_tile_9 APC3_42.chr5.112175162.112175958_tile_9 1 chr5 112175854 112176042 - AGTATTTCAATATCATCATCATCTGAATCATCTAATAGGTCCTTTTCAGAATCAATAGTTTTTTCTGCCTCTTTCTCTTGGTTTTCATTTGATTCTTTAGGCTGCTCTGATTCTGTTTCATTCCCATTGTCATTT Homo sapiens hg19 -CSF1R1_3.chr5.149433644.149433646_tile_1 CSF1R1_3.chr5.149433644.149433646_tile_1 1 chr5 149433616 149433799 + GATAGTTGTTGGGCTGCAGCAAGGGCTGGGCGATATCCCCTTGCTCGCAGCAGGTCAGGTGCTCACTAGAGCTCTCCTCCTCCAGCTCACTGCTGCTGCTGCCGCTGCCACCGCTTCTGCTGCTGCTCGGC Homo sapiens hg19 -CSF1R4.chr5.149453044.149453044_tile_1 CSF1R4.chr5.149453044.149453044_tile_1 1 chr5 149453016 149453189 + CAAGTAGGCACTCTCTGGAAAGCAGAACACACAAGCATCTGGCATTAGTGGGAAGATGTCCTTGTTTATTTGTCCATTTTGTCATCCACCCATTGATCCAGTCCCTGAGCAGCTATGTCAC Homo sapiens hg19 -NPM1.chr5.170837547.170837548_tile_1 NPM1.chr5.170837547.170837548_tile_1 1 chr5 170837493 170837677 + TTTTTTTTCCAGGCTATTCAAGATCTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAGTTTAAACAATTTGTTAAAAAATTTTCCGTCTTATTTCATTTCTGTAACAGTTGATATCTGGCTGTCCTTTTTA Homo sapiens hg19 -EGFR1.chr7.55211080.55211080_tile_1 EGFR1.chr7.55211080.55211080_tile_1 1 chr7 55211052 55211238 + AGAGGAAATATGTACTACGAAAATTCCTATGCCTTAGCAGTCTTATCTAACTATGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTACAGGGTGAGAGGCTGGGATGCCAAGGCTGGGGGT Homo sapiens hg19 -EGFR2.chr7.55221822.55221822_tile_1 EGFR2.chr7.55221822.55221822_tile_1 1 chr7 55221792 55221964 + GGTGCCACCTGCGTGAAGAAGTGTCCCCGTGAGTCCTCCTCTGTGGGCCCTCTAACTGGTCAGGCATCCTTGTCCCGCTCTGTCTCCTGCTGAGCCCTGGAGTATCCCATCTTGGAGAGT Homo sapiens hg19 -EGFR3.chr7.55233043.55233043_tile_1 EGFR3.chr7.55233043.55233043_tile_1 1 chr7 55233019 55233203 + GGAGTCATGGGAGAAAACAACACCCTGGTCTGGAAGTACGCAGACGCCGGCCATGTGTGCCACCTGTGCCATCCAAACTGCACCTACGGGTGAGTGGAAAGTGAAGGAGAACAGAACATTTCCTCTCTTGCAAAT Homo sapiens hg19 -EGFR4.chr7.55241677.55241708_tile_1 EGFR4.chr7.55241677.55241708_tile_1 1 chr7 55241649 55241827 + AGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTGCGTTCGGCACGGTGTATAAGGTAAGGTCCCTGGCACAGGCCTCTGGGCTGGGCCGCAGGGCCTCTCATGGTCTGGTGGGGAGCC Homo sapiens hg19 -EGFR9.chr7.55242418.55242511_tile_1 EGFR9.chr7.55242418.55242511_tile_1 1 chr7 55242388 55242576 + GACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCT Homo sapiens hg19 -EGFR44.chr7.55249005.55249131_tile_1 EGFR44.chr7.55249005.55249131_tile_1 1 chr7 55248879 55249052 + TCTTCACCTGGAAGGGGTCCATGTGCCCCTCCTTCTGGCCACCATGCGAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTG Homo sapiens hg19 -EGFR44.chr7.55249005.55249131_tile_2 EGFR44.chr7.55249005.55249131_tile_2 1 chr7 55249003 55249178 - CAGTTGAGCAGGTACTGGGAGCCAATATTGTCTTTGTGTTCCCGGACATAGTCCAGGAGGCAGCCGAAGGGCATGAGCTGCGTGATGAGCTGCACGGTGGAGGTGAGGCAGATGCCCAGCAGGCGGC Homo sapiens hg19 -EGFR54.chr7.55259514.55259524_tile_1 EGFR54.chr7.55259514.55259524_tile_1 1 chr7 55259486 55259662 + GCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTAAGGAGGTGGCTTTAGGTCAGCCAGCATTTTCCTGACACCAGGGACCAGGCTGCCTTCCCACTAGC Homo sapiens hg19 -MET1.chr7.116339642.116339642_tile_1 MET1.chr7.116339642.116339642_tile_1 1 chr7 116339614 116339792 + AGCCCAGCCAGTGTCCTGACTGTGTGGTGAGCGCCCTGGGAGCCAAAGTCCTTTCATCTGTAAAGGACCGGTTCATCAACTTCTTTGTAGGCAATACCATAAATTCTTCTTATTTCCCAGATCAT Homo sapiens hg19 -MET2.chr7.116340262.116340262_tile_1 MET2.chr7.116340262.116340262_tile_1 1 chr7 116340234 116340420 + AACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGAGCACTGCTTTAATAGGGTAAGTCACATCAGTTCCCCACTTATAAACTGTGAGGTATAAATTAGAAATAAGT Homo sapiens hg19 -MET3.chr7.116411990.116411990_tile_1 MET3.chr7.116411990.116411990_tile_1 1 chr7 116411958 116412127 + GCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATATACCTCAGTGGGTTGT Homo sapiens hg19 -MET4.chr7.116417463.116417464_tile_1 MET4.chr7.116417463.116417464_tile_1 1 chr7 116417431 116417620 + TATATCATGGGACTTTGTTGGACAATGATGGCAAGAAAATTCACTGTGCTGTGAAATCCTTGAACAGTAAGTGGCATTTTATTTAACCATGGAGTATACTTTTGTGGTTTGCAACCTAATAAATAGCTTATAATA Homo sapiens hg19 -MET6.chr7.116423413.116423474_tile_1 MET6.chr7.116423413.116423474_tile_1 1 chr7 116423385 116423555 + TGTATGATAAAGAATACTATAGTGTACACAACAAAACAGGTGCAAAGCTGCCAGTGAAGTGGATGGCTTTGGAAAGTCTGCAAACTCAAAAGTTTACCACCAAGTCAGATGTGGTAAT Homo sapiens hg19 -SMO1.chr7.128845101.128845101_tile_1 SMO1.chr7.128845101.128845101_tile_1 1 chr7 128845073 128845257 + GGTTCGGACAGACAACCCCAAGAGCTGGTACGAGGACGTGGAGGGCTGCGGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCACCAGGACATGCACAGCTACATCGCGGCCTTCGGGGCCGTCACGGGC Homo sapiens hg19 -SMO2.chr7.128846040.128846040_tile_1 SMO2.chr7.128846040.128846040_tile_1 1 chr7 128846010 128846194 + TACGCCCTGATGGCTGGTGTGGTTTGGTTTGTGGTCCTCACCTATGCCTGGCACACTTCCTTCAAAGCCCTGGGCACCACCTACCAGCCTCTCTCGGGCAAGACCTCCTACTTCCACCTGCTCACCTGGTC Homo sapiens hg19 -SMO3.chr7.128846374.128846374_tile_1 SMO3.chr7.128846374.128846374_tile_1 1 chr7 128846348 128846536 + CGTGCTGGCCCCAATCGGCCTGGTGCTCATCGTGGGAGGCTACTTCCTCATCCGAGGTGAGTGAAGACCAGGCCAGGACCAGTTGGGCAACAAAATATACTGGGCACTTGCTGCCAGTACTGGGAGCTGCCAGCACG Homo sapiens hg19 -SMO4.chr7.128850341.128850341_tile_1 SMO4.chr7.128850341.128850341_tile_1 1 chr7 128850311 128850499 + GCACCTGGGTCTGGACCAAGGCCACGCTGCTCATCTGGAGGCGTACCTGGTGCAGGTGGGCATGGCAGCCAGCCCCTCCTGCCCTGCCCGCCTCACCCTCAGCCTTGGGACCCCATCTTTAGGTTTTGTCGGGTCCTG Homo sapiens hg19 -SMO5.chr7.128851593.128851593_tile_1 SMO5.chr7.128851593.128851593_tile_1 1 chr7 128851563 128851734 + GTCACCCCTGTGGCAACTCCAGGTATGAGAGTTCAAGCTTCTGGAGGAAGGTGGGGGGAGCACAGAGGCTGGGGGCTTCTGGGACTGGAGTACAGGGGCTGTCGGAGGAGGAGGAAGAG Homo sapiens hg19 -BRAF1.chr7.140453121.140453193_tile_1 BRAF1.chr7.140453121.140453193_tile_1 1 chr7 140453093 140453267 + CACTCCATCGAGATTTCACTGTAGCTAGACCAAAATCACCTATTTTTACTGTGAGGTCTTCATGAAGAAATATATCTGAGGTGTAGTAAGTAAAGGAAAACAGTAGATCTCATTTTCCTATC Homo sapiens hg19 -BRAF28.chr7.140481397.140481478_tile_1 BRAF28.chr7.140481397.140481478_tile_1 1 chr7 140481369 140481545 + ACTGTTCCAAATGATCCAGATCCAATTCTTTGTCCCACTGTAATCTGCCCATCAGGAATCTCCCAATCATCACTCGAGTCCCGTCTACCAAGTGTTTTCTTGATAAAAACAGTAAAAAAGTCA Homo sapiens hg19 -FGFR1_1.chr8.38282209.38282209_tile_1 FGFR1_1.chr8.38282209.38282209_tile_1 1 chr8 38282183 38282360 + GGGGACCGCTCTGTGGAAGATGGGAGAGGAGGCACTTGTCATGGGGACCTTGCCATGGCTAAAGAGGGGTGGGCTCACCTGCGCCCCACTTGGCTTTCCCAGTGATGGGTTGTAAACCTCCCAGCAC Homo sapiens hg19 -FGFR1_2.chr8.38285938.38285938_tile_1 FGFR1_2.chr8.38285938.38285938_tile_1 1 chr8 38285908 38286090 + TCCGAGGAGGGGAGAGCATCTATGGGAAGAAGAAGGGGCACTGAGGTTCCTCCTAGGGACCCCTAGATTTCACCAAGGCTAGTGCAGTTCCAGATGAACACGGACACCCTCCCCATGGGGATCCCAGTC Homo sapiens hg19 -JAK2_1.chr9.5073769.5073770_tile_1 JAK2_1.chr9.5073769.5073770_tile_1 1 chr9 5073737 5073923 + TATGTGTCTGTGGAGACGAGAGTAAGTAAAACTACAGGCTTTCTAATGCCTTTCTCAGAGCATCTGTTTTTGTTTATATAGAAAATTCAGTTTCAGGATCACAGCTAGGTGTCAGTGTAAACTATAATTT Homo sapiens hg19 -CDKN2A1.chr9.21971153.21971187_tile_1 CDKN2A1.chr9.21971153.21971187_tile_1 1 chr9 21971123 21971308 + GGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCC Homo sapiens hg19 -ABL1_1.chr9.133738330.133738364_tile_1 ABL1_1.chr9.133738330.133738364_tile_1 1 chr9 133738302 133738491 + CCATGAAGCACAAGCTGGGCGGGGGCCAGTACGGGGAGGTGTACGAGGGCGTGTGGAAGAAATACAGCCTGACGGTGGCCGTGAAGACCTTGAAGGTAGGCTGGGACTGCCGGGGGTGCCCAGGGTACGTGGGGCAAG Homo sapiens hg19 -ABL1_9.chr9.133747520.133747520_tile_1 ABL1_9.chr9.133747520.133747520_tile_1 1 chr9 133747476 133747664 + TTTCCTTCTGCAGGAGGACACCATGGAGGTGGAAGAGTTCTTGAAAGAAGCTGCAGTCATGAAAGAGATCAAACACCCTAACCTGGTGCAGCTCCTTGGTGAGTAAGCCCGGGGCTCTGAAGAGAGGGTCTCGCGCCGC Homo sapiens hg19 -ABL1_10.chr9.133748283.133748414_tile_1 ABL1_10.chr9.133748283.133748414_tile_1 1 chr9 133748157 133748327 - CCCGTAGGTCATGAACTCAGTGATGATATAGAACGGGGGCTCCCGGGTGCAGACCCCTGCCAACAAGACAACGAGGACTTCAACACGTGGCTCCGCTCCCAACTGAACAAACAACT Homo sapiens hg19 -ABL1_10.chr9.133748283.133748414_tile_2 ABL1_10.chr9.133748283.133748414_tile_2 1 chr9 133748277 133748457 + GAACCTCCTGGACTACCTGAGGGAGTGCAACCGGCAGGAGGTGAACGCCGTGGTGCTGCTGTACATGGCCACTCAGATCTCGTCAGCCATGGAGTACCTGGAGAAGAAAAACTTCATCCACAGGTAGGGGCCT Homo sapiens hg19 -ABL1_16.chr9.133750356.133750356_tile_1 ABL1_16.chr9.133750356.133750356_tile_1 1 chr9 133750328 133750516 + GCCCATGCTGGAGCCAAGTTCCCCATCAAATGGACTGCACCCGAGAGCCTGGCCTACAACAAGTTCTCCATCAAGTCCGACGTCTGGGGTAAGGGCTGCTGCTGCACTGAAGTGGTCCTTCCTGACTACAGGAGGGTT Homo sapiens hg19 -NOTCH1_1.chr9.139397768.139397768_tile_1 NOTCH1_1.chr9.139397768.139397768_tile_1 1 chr9 139397740 139397928 + CCAGGTAGACGATGGAGCTGGGCGGACAATCAGAGAGGGGCTGGGACCCGAGGCTTCCTCCTCCCCCGCCCACCGGCCAGGGATGCTGCCGCAGGACACTGAGGCCCATGACGCCACAGTCAGGACATGGTGAGGC Homo sapiens hg19 -NOTCH1_2.chr9.139399344.139399422_tile_1 NOTCH1_2.chr9.139399344.139399422_tile_1 1 chr9 139399316 139399485 + GCAGCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGCGCAGCTGCTCCGGCGGCATCAGCACCACCACCACCAGCGTGCCGGCCGCCAGCCTCTCGGGTACATGCTCCGC Homo sapiens hg19 -RET1.chr10.43609078.43609104_tile_1 RET1.chr10.43609078.43609104_tile_1 1 chr10 43609048 43609226 + CTGCTTCCCTGAGGAGGAGAAGTGCTTCTGCGAGCCCGAAGACATCCAGGGTGAGTGGGTGGCGGCCGGGACCACCACCACCTCCCAGCCCCACAGAGGTCTCAACAGCACATCTGAGGTCCCAACAA Homo sapiens hg19 -RET2_9.chr10.43609940.43609950_tile_1 RET2_9.chr10.43609940.43609950_tile_1 1 chr10 43609902 43610075 - TGGCTTGTGGGCAAACTTGTGGTAGCAGTGGATGCAGAAGGCAGACAGCAGCACCGAGACGATGAAGGAGAAGAGGACAGCGGCTGCGATCACCGTGCGGCACAGCTCGTCGCACAGTGG Homo sapiens hg19 -RET10.chr10.43613840.43613840_tile_1 RET10.chr10.43613840.43613840_tile_1 1 chr10 43613810 43613998 + CGAGTGAGCTGCGAGACCTGCTGTCAGAGTTCAACGTCCTGAAGCAGGTCAACCACCCACATGTCATCAAATTGTATGGGGCCTGCAGCCAGGATGGTAAGGCCAGCTGCAGGGTGAGGTGGGCAGCCACTGCACCCAG Homo sapiens hg19 -RET11_12.chr10.43615567.43615569_tile_1 RET11_12.chr10.43615567.43615569_tile_1 1 chr10 43615533 43615703 + CCTGGTAGCTGAGGGGCGGAAGATGAAGATTTCGGATTTCGGCTTGTCCCGAGATGTTTATGAAGAGGATTCCTACGTGAAGAGGAGCCAGGTGCCCAGTCCCGGGGATGAGGCGGGG Homo sapiens hg19 -RET13.chr10.43617416.43617416_tile_1 RET13.chr10.43617416.43617416_tile_1 1 chr10 43617388 43617564 + ATGGCAATTGAATCCCTTTTTGATCATATCTACACCACGCAAAGTGATGTGTAAGTGTGGGTGTTGCTCTCTTGGGGTGGAGGTTACAGAAACACCCTTATACATGTAGTGGGGCCACGACGC Homo sapiens hg19 -PTEN1.chr10.89624242.89624244_tile_1 PTEN1.chr10.89624242.89624244_tile_1 1 chr10 89624214 89624388 + CAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACCTTTCTGTCACTCTCTTAGAACGTGG Homo sapiens hg19 -PTEN3.chr10.89685307.89685307_tile_1 PTEN3.chr10.89685307.89685307_tile_1 1 chr10 89685275 89685459 + ATATACAATCTGTAAGTATGTTTTCTTATTTGTATGCTTGCAAATATCTTCTAAAACAACTATTAAGTGAAAGTTATCTGCTTGTTAGAGTGAGGTAGAGTTAAAGATACATTTTAACAGAATTGTATT Homo sapiens hg19 -PTEN4.chr10.89711893.89711900_tile_1 PTEN4.chr10.89711893.89711900_tile_1 1 chr10 89711865 89712039 + GTCAGAGGCGCTATGTGTATTATTATAGCTACCTGTTAAAGAATCATCTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACT Homo sapiens hg19 -PTEN7.chr10.89717615.89717772_tile_1 PTEN7.chr10.89717615.89717772_tile_1 1 chr10 89717489 89717668 + ATATTGCTGATATTAATCATTAAAATCGTTTTTGACAGTTTGACAGTTAAAGGCATTTCCTGTGAAATAATACTGGTATGTATTTAACCATGCAGATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 -PTEN7.chr10.89717615.89717772_tile_2 PTEN7.chr10.89717615.89717772_tile_2 1 chr10 89717615 89717801 - TTTAGCATCTTGTTCTGTTTGTGGAAGAACTCTACTTTGATATCACCACACACAGGTAACGGCTGAGGGAACTCAAAGTACATGAACTTGTCTTCCCGTCGTGTGGGTCCTGAATTGGAGGAATATATCTTCACC Homo sapiens hg19 -PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 1 chr10 89720684 89720870 + CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 -PTEN13.chr10.89720716.89720852_tile_2 PTEN13.chr10.89720716.89720852_tile_2 1 chr10 89720814 89720991 - TTCTTCATCAGCTGTACTCCTAGAATTAAACACACATCACATACATACAAGTCAACAACCCCCACAAAATGTTTAATTTAACTGACCTTAAAATTTGGAGAAAAGTATCGGTTGGCTTT Homo sapiens hg19 -FGFR2_1.chr10.123258034.123258034_tile_1 FGFR2_1.chr10.123258034.123258034_tile_1 1 chr10 123258006 123258184 + GATTTATGATATTCTTGTGTTTCCCAATCATCTTCATCATCTCCATCTCTGACACCAGATCAGAAAGGTCTTTCTCTGTGGCATCATCTATGAACAGTAGGCATATTCACAAATCAGTTCATTTC Homo sapiens hg19 -FGFR2_2.chr10.123274774.123274803_tile_1 FGFR2_2.chr10.123274774.123274803_tile_1 1 chr10 123274746 123274930 + CAGTAAATGGCTATCTCCAGGTAGTCTGGGGAAGCTGTAATCTCCTTTTCTCTTCCAGGCGCTAGATTGCAGATCACAGGAGGAGGAACAGATAAGCAGGCCATAGAGTTAGCACACCAGACTGACGCATC Homo sapiens hg19 -FGFR2_5.chr10.123279503.123279677_tile_1 FGFR2_5.chr10.123279503.123279677_tile_1 1 chr10 123279385 123279555 + AACAGGAAATCAAAGAACCTGTGGCCAAACCCATGAAGGAGACCCCAGTTGTGGGTACCTTTAGATTCAGAAAGTCCTCACCTTGAGAACCTTGAGGTAGGGCAGCCCGTCGGGCCC Homo sapiens hg19 -FGFR2_5.chr10.123279503.123279677_tile_2 FGFR2_5.chr10.123279503.123279677_tile_2 1 chr10 123279471 123279640 - ACGTAGAGTTTGTCTGCAAGGTTTACAGTGATGCCCAGCCCCACATCCAGTGGATCAAGCACGTGGAAAAGAACGGCAGTAAATACGGGCCCGACGGGCTGCCCTACCTCAAGGTT Homo sapiens hg19 -FGFR2_5.chr10.123279503.123279677_tile_3 FGFR2_5.chr10.123279503.123279677_tile_3 1 chr10 123279587 123279769 + TCTCCTCCGACCACTGTGGAGGCATTTGCCGGCAGTCCGGCTTGGAGGATGGGCCGGTGAGGCGATCGCTCTGGTGGAGAGAGGGAAGAAAGGAGGAGTGGGGATGGGAGAATGAGAGACCAATAAATA Homo sapiens hg19 -HRAS1.chr11.533873.533875_tile_1 HRAS1.chr11.533873.533875_tile_1 1 chr11 533843 534021 + CCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAATCCTGCAGGAGGACAGGGCTCAGGGACCCCCTCAGGACCTTCCGTGGGGGGA Homo sapiens hg19 -HRAS6.chr11.534285.534289_tile_1 HRAS6.chr11.534285.534289_tile_1 1 chr11 534251 534434 + GCCCACACCGCCGGCGCCCACCACCACCAGCTTATATTCCGTCATCGCTCCTCAGGGGCCTGCGGCCCGGGGTCCTCCTACAGGGTCTCCTGCCCCACCTGCCAAGGAGGGCCCTGCTCAGCCAGGCCCAGGC Homo sapiens hg19 -ATM1.chr11.108117847.108117848_tile_1 ATM1.chr11.108117847.108117848_tile_1 1 chr11 108117817 108117989 + TGTCACCAGGTACAGTAAGTAGGTCATGTCACATTTAGAAATTTCCTGTTAATTTTTTTTTTAAACTGGGCATTTTGGGCTTTTAAAACCTGTGTTCTCACAAAAAGCCTATAAAAT Homo sapiens hg19 -ATM2.chr11.108119823.108119823_tile_1 ATM2.chr11.108119823.108119823_tile_1 1 chr11 108119793 108119963 + TTGTGCCTTGGTAAAGTGTTACCATTTTCTCATTCAGTGTCATTTTAATCTCTTGTATGTTATTTTTCAGAAAACTTTCAGTGGAATCCTTTCATCTCAACCAGAACTAAGTCATTT Homo sapiens hg19 -ATM3.chr11.108123551.108123551_tile_1 ATM3.chr11.108123551.108123551_tile_1 1 chr11 108123513 108123683 + AGTAATTTTCCTCATCTTGTACTGGAGAAAATTCTTGTGAGTCTCACTATGAAAAACTGTAAAGCTGCAATGAATTTTTTCCAAAGCGTGCCAGAATGGTATGTTATCTAATA Homo sapiens hg19 -ATM4.chr11.108137973.108138003_tile_1 ATM4.chr11.108137973.108138003_tile_1 1 chr11 108137939 108138126 + TAATGGAGGTGGAGGATCAGTCATCCATGAATCTATTTAACGATTACCCTGATAGTAGTGTTAGTGATGCAAACGAACCTGGAGAGAGCCAAAGTACCATAGGTAAATACATATTTACTACTTGGGATT Homo sapiens hg19 -ATM6.chr11.108155132.108155132_tile_1 ATM6.chr11.108155132.108155132_tile_1 1 chr11 108155104 108155281 + GGCACAGCAAAGAGAGACTGCTACCAAGGTCTATGATATGCTTAAAAGTGAAAACTTATTGGGAAAACAGGTATGGCTTCAATTTTTATGTACTTTTCATTCCCTGAATGATATGAGATAT Homo sapiens hg19 -ATM7.chr11.108170476.108170479_tile_1 ATM7.chr11.108170476.108170479_tile_1 1 chr11 108170442 108170618 + GGGTCCTATAGATTTCTCTACCATAGCTATACAACATAGTAAAGATGCATCTTATACCAAGGCCCTTAAGTTATTTGAAGATAAAGAACTTCAGTGGACCTTCATAATGCTGACCTACCTGAA Homo sapiens hg19 -ATM9.chr11.108172421.108172421_tile_1 ATM9.chr11.108172421.108172421_tile_1 1 chr11 108172391 108172571 + TTAGCCACAAAGACTGGACATAGTTTCTGGGAGATTTATAAGATGACAACAGATCCAATGCTGGCCTATCTACAGCCTTTTAGAACATCAAGAAAAAAGGTCTCTTAAGTAATAAATGTTTATTGAA Homo sapiens hg19 -ATM10.chr11.108173640.108173640_tile_1 ATM10.chr11.108173640.108173640_tile_1 1 chr11 108173612 108173801 + AAATCTGTGGATTCCTCTAAGTGAAAATCATGACATTTGGATAAAGACACTGACTTGTGCTTTTTTGGACAGTGGAGGCACAAAATGTGAAATTCTTCAATTATTAAAGCCAATGTGTGAAGTAAGAAGATTAATT Homo sapiens hg19 -ATM11.chr11.108180945.108180945_tile_1 ATM11.chr11.108180945.108180945_tile_1 1 chr11 108180915 108181101 + AAGTTGCCAAGGTAGCTCAGTCTTGTGCTGCTCACTTTACAGCTTTACTCTATGCAGAAATCTATGCAGATAAGAAAAGTATGGATGATCAAGAGAAAAGGTAATGGAATTTAGAATTTTTGGTTTTTAAAA Homo sapiens hg19 -ATM12.chr11.108200958.108200961_tile_1 ATM12.chr11.108200958.108200961_tile_1 1 chr11 108200926 108201096 + TTCAGCGAGAGCTGGAGTTGGATGAATTAGCCCTGCGTGCACTGAAAGAGGATCGTAAACGCTTCTTATGTAAAGCAGTTGAAAATTATATCAACTGCTTATTAAGTGGAGAAGA Homo sapiens hg19 -ATM14.chr11.108204681.108204681_tile_1 ATM14.chr11.108204681.108204681_tile_1 1 chr11 108204651 108204823 + TACTATGGAAATTAAGGTAATTTGCAATTAACTCTTGATTTTTTTTAAACTAAATTTTTTTTATTAGATTGAACCATTTGAAATAGTATTTTTATGTAGGTCAAAATTGGTTAAATA Homo sapiens hg19 -ATM15.chr11.108205769.108205769_tile_1 ATM15.chr11.108205769.108205769_tile_1 1 chr11 108205739 108205928 + AGGTGTAAATTTACCAAAAATAATAGATTGTGTAGGTTCCGATGGCAAGGAGAGGAGACAGCTTGTTAAGGTGAGCCTTCCCTTCTCTGGCTTAGCCCTTAGAGTTTTAGTGATGAAAATTTTTAGTTCATATT Homo sapiens hg19 -ATM16.chr11.108206594.108206594_tile_1 ATM16.chr11.108206594.108206594_tile_1 1 chr11 108206566 108206750 + GATGCTGTCATGCAACAGGTCTTCCAGATGTGTAATACATTACTGCAGAGAAACACGGAAACTAGGAAGAGGAAATTAACTATCTGTACTTATAAGGTAACTATTTGTACTTCTGTTAGTTCACCAAAAAC Homo sapiens hg19 -ATM17.chr11.108218089.108218089_tile_1 ATM17.chr11.108218089.108218089_tile_1 1 chr11 108218061 108218247 + TCTAGGTAAGTAATAAAATCTATGTATCTATTCTTTTTAGTAAATATTTGGTCATCATGGAATGTTGTTTGCCTACCAAGATATTACAAATATAAGAGACAGATAAATTGAAGCAGTAAATATTGGGTTTTTT Homo sapiens hg19 -ATM18.chr11.108225590.108225590_tile_1 ATM18.chr11.108225590.108225590_tile_1 1 chr11 108225562 108225751 + AACCATTGTAGAGGTAAAGTATTTTATAAGGAAGACTTTATTTTTTTTCTTACCAGGTAGACTGTGTATCTCATCAGGAAGTCACTGATGTGAAGAGCACTGCTTCATTTTAACATAGGGGGATGTGGCTGGGCAGC Homo sapiens hg19 -ATM19.chr11.108236086.108236203_tile_1 ATM19.chr11.108236086.108236203_tile_1 1 chr11 108236058 108236241 + ACGTGTCTTAATGAGACTACAAGAGAAACTGAAAGGAGTGGAAGAAGGCACTGTGCTCAGTGTTGGTGGACAAGTGAATTTGCTCATACAGCAGGCCATAGACCCCAAAAATCTCAGCCGACTTTTCCCAG Homo sapiens hg19 -KRAS1.chr12.25378562.25378562_tile_1 KRAS1.chr12.25378562.25378562_tile_1 1 chr12 25378532 25378717 + TTGCTGATGTTTCAATAAAAGGAATTCCATAACTTCTTGCTAAGTCCTGAGCCTGTTTTGTGTCTACTGTTCTAGAAGGCAAATCACATTTATTTCCTACTAGGACCATAGGTACATCTTCAGAGTCCTTA Homo sapiens hg19 -KRAS2.chr12.25380275.25380283_tile_1 KRAS2.chr12.25380275.25380283_tile_1 1 chr12 25380245 25380427 + CCTCTTGACCTGCTGTGTCGAGAATATCCAAGAGACAGGTTTCTCCATCAATTACTACTTGCTTCCTGTAGGAATCCTGAGAAGGGAGAAACACAGTCTGGATTATTACAGTGCACCTTTTACTTCAA Homo sapiens hg19 -KRAS7.chr12.25398255.25398285_tile_1 KRAS7.chr12.25398255.25398285_tile_1 1 chr12 25398225 25398414 + TGTATCGTCAAGGCACTCTTGCCTACGCCACCAGCTCCAACTACCACAAGTTTATATTCAGTCATTTTCAGCAGGCCTTATAATAAAAATAATGAAAATGTGACTATATTAGAACATGTCACACATAAGGTTA Homo sapiens hg19 -PTPN11_1.chr12.112888163.112888211_tile_1 PTPN11_1.chr12.112888163.112888211_tile_1 1 chr12 112888135 112888323 + TGGTGATTACTATGACCTGTATGGAGGGGAGAAATTTGCCACTTTGGCTGAGTTGGTCCAGTATTACATGGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTCATTGAGCTTAAATATCCTCTGAACTGT Homo sapiens hg19 -PTPN11_10.chr12.112926884.112926888_tile_1 PTPN11_10.chr12.112926884.112926888_tile_1 1 chr12 112926856 112927032 + GGTCAGGGATGGTCCAGACAGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATATTGAAACACTACAGCGCAGGATTGAAGAAGAGCAGGTACCAGCCTGAGGGCTGGCATGCGG Homo sapiens hg19 -HNF1A_1.chr12.121431413.121431414_tile_1 HNF1A_1.chr12.121431413.121431414_tile_1 1 chr12 121431385 121431558 + GTGGGGCCCAGCATCCCAGCAGATCCTGTTCCAGGCCTATGAGAGGCAGAAGAACCCTAGCAAGGAGGAGCGAGAGACGCTAGTGGAGGAGTGCAATAGGTACAACGGCGGGCGGGAAACAG Homo sapiens hg19 -HNF1A_3.chr12.121432070.121432070_tile_1 HNF1A_3.chr12.121432070.121432070_tile_1 1 chr12 121432042 121432221 + GCGCAAAGAAGAAGCCTTCCGGCACAAGCTGGCCATGGACACGTACAGCGGGCCCCCCCCAGGGCCAGGCCCGGGACCTGCGCTGCCCGCTCACAGCTCCCCTGGCCTGCCTCCACCTGCCCTCTCCCCC Homo sapiens hg19 -FLT3_1.chr13.28592620.28592653_tile_1 FLT3_1.chr13.28592620.28592653_tile_1 1 chr13 28592590 28592766 + CATAGTTGGAATCACTCATGATATCTCGAGCCAATCCAAAGTCACATATCTTCACCACTTTCCCGTGGGTGACAAGCACGTTCCTGGCGGCCAGGTCTCTGTGAACACACTGTCAAGAATGA Homo sapiens hg19 -FLT3_13.chr13.28602329.28602329_tile_1 FLT3_13.chr13.28602329.28602329_tile_1 1 chr13 28602295 28602464 + GTGTGCACGCCCCCAGCAGGTTCACAATATTCTCGTGGCTTCCCAGCTGGGTCATCATCTTGAGTTCTGACATGAGTGCCTCTCTTTCAGAGCTGTCTGCTTTTTCTGTCAAAGAA Homo sapiens hg19 -FLT3_14.chr13.28608244.28608341_tile_1 FLT3_14.chr13.28608244.28608341_tile_1 1 chr13 28608214 28608402 + ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTAAATTGCTTCAGAGATGAAATGATGAGTCA Homo sapiens hg19 -FLT3_22.chr13.28610138.28610138_tile_1 FLT3_22.chr13.28610138.28610138_tile_1 1 chr13 28610098 28610267 - TATAGGAGTGAACCACTATGCCCAGCCAGTGAGCTTATTTCACACGTTCTTTTCTATAGGGAAACCTCAAGTGCTCGCAGAAGCATCGGCAAGTCAGGCGTCCTGTTTCTCGGATGG Homo sapiens hg19 -RB1_1.chr13.48919244.48919244_tile_1 RB1_1.chr13.48919244.48919244_tile_1 1 chr13 48919156 48919336 + ATTTACTTTTTTCTATTCTTTCCTTTGTAGTGTCCATAAATTCTTTAACTTACTAAAAGAAATTGATACCAGTACCAAAGTTGATAATGCTATGTCAAGACTGTTGAAGAAGTATGATGTATTG Homo sapiens hg19 -RB1_2.chr13.48923148.48923148_tile_1 RB1_2.chr13.48923148.48923148_tile_1 1 chr13 48923120 48923296 + TTATTAGCTAAAGGTAAGTTCATTATATTTATTAAATGCTAATATTTCAAATGTAATAATTAAATTGGCATTCCTTTGGACTAAATTCCCCAATTTTTATTGAGTAATGTACTCCTCCCTCAT Homo sapiens hg19 -RB1_3.chr13.48942685.48942685_tile_1 RB1_3.chr13.48942685.48942685_tile_1 1 chr13 48942655 48942826 + ACGAAAAAGTAACCTTGATGAAGAGGTGAATGTAATTCCTCCACACACTCCAGTTAGGTATGAATTTTCCTACTTTTAATTATATTATAATTTTGTTATTCATGGCTTTATAGTG Homo sapiens hg19 -RB1_4.chr13.48955538.48955550_tile_1 RB1_4.chr13.48955538.48955550_tile_1 1 chr13 48955504 48955684 + TAGAACGATGTGAACATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGAAATTCATTCATGTGCATATGGCTAACAAATTATTGTTAGTGAGAGGTGTTTCTTA Homo sapiens hg19 -RB1_6.chr13.49027168.49027168_tile_1 RB1_6.chr13.49027168.49027168_tile_1 1 chr13 49027112 49027288 + TTTGATCTTATTAAACAATCAAAGGACCGAGAAGGACCAACTGATCACCTTGAATCTGCTTGTCCTCTTAATCTTCCTCTCCAGAATAATCACACTGCAGCAGATATGTAAGCAAAATATA Homo sapiens hg19 -RB1_7.chr13.49033843.49033846_tile_1 RB1_7.chr13.49033843.49033846_tile_1 1 chr13 49033813 49033989 + TCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGACCCTTTTCCAGCACACCCTGCAGAATGAGTATGAACTCATGAGAGACAGGCATTT Homo sapiens hg19 -RB1_8.chr13.49037877.49037877_tile_1 RB1_8.chr13.49037877.49037877_tile_1 1 chr13 49037815 49037985 + TTTACATCAATTTATTTACTAGATTATGATGTGTTCCATGTATGGCATATGCAAAGTGAAGAATATAGACCTTAAATTCAAAATCATTGTAACAGCATACAAGGATCTTCCTCA Homo sapiens hg19 -RB1_9.chr13.49039164.49039164_tile_1 RB1_9.chr13.49039164.49039164_tile_1 1 chr13 49039132 49039304 + AAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCCACCAGGGTAGGTCAAAAGTATCCTTTGATTGGAAAA Homo sapiens hg19 -AKT1.chr14.105246455.105246455_tile_1 AKT1.chr14.105246455.105246455_tile_1 1 chr14 105246429 105246600 + CTCACGTTGGTCCACATCCTGCGGCCGCTCCTTGTAGCCAATGAAGGTGCCATCATTCTTGAGGAGGAAGTAGCGTGGCCGCCAGGTCTTGATGTACTCCCCTACAGACGTGCGGGTGGTGA Homo sapiens hg19 -CDH1_1.chr16.68835649.68835650_tile_1 CDH1_1.chr16.68835649.68835650_tile_1 1 chr16 68835613 68835782 + TGGGCACAGATGGTGTGATTACAGTCAAAAGGCCTCTACGGTTTCATAACCCACAGATCCATTTCTTGGTCTACGCCTGGGACTCCACCTACAGAAAGTTTTCCACCAAAGTCACGCTGAAT Homo sapiens hg19 -CDH1_2.chr16.68846137.68846137_tile_1 CDH1_2.chr16.68846137.68846137_tile_1 1 chr16 68846109 68846283 + CGATAATCCTCCGATCTTCAATCCCACCACGGTAATTCTATAACTCCTTAGAGGGTTTCCAAAGAAAGGTCTTTTGTTGTTCATGAACTAAGTGTCACCACTGCTCATGGGCGAAGTCTTT Homo sapiens hg19 -CDH1_3.chr16.68847274.68847277_tile_1 CDH1_3.chr16.68847274.68847277_tile_1 1 chr16 68847246 68847422 + ACTGATGCTGATGCCCCCAATACCCCAGCGTGGGAGGCTGTATACACCATATTGAATGATGATGGTGGACAATTTGTCGTCACCACAAATCCAGTGAACAACGATGGCATTTTGAAAACAGCA Homo sapiens hg19 -TP53_1.chr17.7574003.7574021_tile_1 TP53_1.chr17.7574003.7574021_tile_1 1 chr17 7573977 7574147 + CGGAACATCTCGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATACACAGTACCTGAGTTAAAAGATGGTTCAAGTTACAATTGTTTGACTTTATG Homo sapiens hg19 -TP53_3.chr17.7577022.7577129_tile_1 TP53_3.chr17.7577022.7577129_tile_1 1 chr17 7576996 7577166 + CGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCG Homo sapiens hg19 -TP53_17.chr17.7577523.7577574_tile_1 TP53_17.chr17.7577523.7577574_tile_1 1 chr17 7577495 7577683 + GGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGA Homo sapiens hg19 -TP53_31_59.chr17.7578190.7578536_tile_1 TP53_31_59.chr17.7578190.7578536_tile_1 1 chr17 7578064 7578234 + AGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTA Homo sapiens hg19 -TP53_31_59.chr17.7578190.7578536_tile_2 TP53_31_59.chr17.7578190.7578536_tile_2 1 chr17 7578156 7578325 - CTGATTGCTCTTAGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCC Homo sapiens hg19 -TP53_31_59.chr17.7578190.7578536_tile_3 TP53_31_59.chr17.7578190.7578536_tile_3 1 chr17 7578246 7578415 + TGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCG Homo sapiens hg19 -TP53_31_59.chr17.7578190.7578536_tile_4 TP53_31_59.chr17.7578190.7578536_tile_4 1 chr17 7578346 7578515 - GTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCG Homo sapiens hg19 -TP53_31_59.chr17.7578190.7578536_tile_5 TP53_31_59.chr17.7578190.7578536_tile_5 1 chr17 7578468 7578645 + CCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGA Homo sapiens hg19 -TP53_60.chr17.7579358.7579403_tile_1 TP53_60.chr17.7579358.7579403_tile_1 1 chr17 7579324 7579507 + GCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAG Homo sapiens hg19 -TP53_64.chr17.7579882.7579882_tile_1 TP53_64.chr17.7579882.7579882_tile_1 1 chr17 7579852 7580032 + GCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAG Homo sapiens hg19 -ERBB2_1.chr17.37880219.37880261_tile_1 ERBB2_1.chr17.37880219.37880261_tile_1 1 chr17 37880191 37880361 + TGTTGAGGGAAAACACATCCCCCAAAGCCAACAAAGAAATCTTAGACGTAAGCCCCTCCACCCTCTCCTGCTAGGAGGACAGGAAGGACCCCATGGCTGCAGGTCTGGGCTCTGGTCT Homo sapiens hg19 -ERBB2_4.chr17.37880993.37881012_tile_1 ERBB2_4.chr17.37880993.37881012_tile_1 1 chr17 37880963 37881151 + CGTGATGGCTGGTGTGGGCTCCCCATATGTCTCCCGCCTTCTGGGCATCTGCCTGACATCCACGGTGCAGCTGGTGACACAGCTTATGCCCTATGGCTGCCTCTTAGACCATGTCCGGGAAAACCGCGGACGCCTGGG Homo sapiens hg19 -ERBB2_13.chr17.37881332.37881440_tile_1 ERBB2_13.chr17.37881332.37881440_tile_1 1 chr17 37881298 37881482 + GCGGCTCGTACACAGGGACTTGGCCGCTCGGAACGTGCTGGTCAAGAGTCCCAACCATGTCAAAATTACAGACTTCGGGCTGGCTCGGCTGCTGGACATTGACGAGACAGAGTACCATGCAGATGGGGGCA Homo sapiens hg19 -SMAD4_1.chr18.48575169.48575170_tile_1 SMAD4_1.chr18.48575169.48575170_tile_1 1 chr18 48575131 48575301 + TTTGACTTAAAATGTGATAGTGTCTGTGTGAATCCATATCACTACGAACGAGTTGTATCACCTGGAATTGGTAAGTAGACTTTGCTTTCATCCTAAGAAACATAAAGGGAAA Homo sapiens hg19 -SMAD4_2.chr18.48581198.48581198_tile_1 SMAD4_2.chr18.48581198.48581198_tile_1 1 chr18 48581168 48581346 + AGGGACAGCCATCGTTGTCCACTGAAGGACATTCAATTCAAACCATCCAGCATCCACCAAGTAATCGTGCATCGACAGAGACATACAGCACCCCAGCTCTGTTAGCCCCATCTGAGTCTAATGC Homo sapiens hg19 -SMAD4_3.chr18.48584560.48584560_tile_1 SMAD4_3.chr18.48584560.48584560_tile_1 1 chr18 48584528 48584714 + GGGCCTCAGCCAGGACAGCAGCAGAATGGATTTACTGGTCAGCCAGCTACTTACCATCATAGTATGTACATACTTTAAAAAATCTTTTAAATAGTTGAGAAAAAAGTAGGCAGCCTTTATAAAAGCAAATTAAC Homo sapiens hg19 -SMAD4_4.chr18.48586262.48586262_tile_1 SMAD4_4.chr18.48586262.48586262_tile_1 1 chr18 48586234 48586416 + CCAGCCTCCCATTTCCAATCATCCTGGTAAGTGTATTTCAAAATTGATTTCCTGTATTTAGATTGATTTAGTGGTGATTGAAACGCACAAACACAGGCTTTAATGGAATTATGGGGTCACTTCTCAGAT Homo sapiens hg19 -SMAD4_5.chr18.48591826.48591919_tile_1 SMAD4_5.chr18.48591826.48591919_tile_1 1 chr18 48591796 48591982 + TTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGCCCTATTGTTACTGTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAATGTCCACAGGAC Homo sapiens hg19 -SMAD4_11.chr18.48593405.48593405_tile_1 SMAD4_11.chr18.48593405.48593405_tile_1 1 chr18 48593377 48593547 + AAGGTGTGCAGTTGGAATGTAAAGGTGAAGGTGATGTTTGGGTCAGGTGCCTTAGTGACCACGCGGTCTTTGTACAGAGTTACTACTTAGACAGAGAAGCTGGGCGTGCACCTGGAGA Homo sapiens hg19 -SMAD4_12.chr18.48603032.48603094_tile_1 SMAD4_12.chr18.48603032.48603094_tile_1 1 chr18 48602998 48603168 + TGTCATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGCCCAGGATCAGTAGGTGGAATAGCTCCA Homo sapiens hg19 -SMAD4_15.chr18.48604668.48604754_tile_1 SMAD4_15.chr18.48604668.48604754_tile_1 1 chr18 48604638 48604808 + CGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTGGGGACCGGATTACCCAAGACAGAGCATCAAAGAAACACCTTGCTGGATTGAAATTCACTTACACCGGGCCCTCCAGC Homo sapiens hg19 -STK11_1.chr19.1207021.1207092_tile_1 STK11_1.chr19.1207021.1207092_tile_1 1 chr19 1206993 1207169 + CCAGCCGCGCCGCAAGCGGGCCAAGCTCATCGGCAAGTACCTGATGGGGGACCTGCTGGGGGAAGGCTCTTACGGCAAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGCAGGAGGGCCGT Homo sapiens hg19 -STK11_4.chr19.1220487.1220502_tile_1 STK11_4.chr19.1220487.1220502_tile_1 1 chr19 1220459 1220638 + CCGACCTGGGCGTGGCCGAGGTAGGCACGTGCTAGGGGGGGCCCTGGGGCGCCCCCTCCCGGGCACTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTTCGCGGCGGACGACACCTGCCG Homo sapiens hg19 -STK11_8.chr19.1221264.1221319_tile_1 STK11_8.chr19.1221264.1221319_tile_1 1 chr19 1221232 1221407 - CCCGCCTCCCTGGGGCTGCGGGCAGAGGGATGAGGCTCCCACCTTTCAGCAGGTCAGAGAGCGGGGGGCCACAGTCGCCCGGGATGGCGTAGCTCCCCTTCCCGATGTTCTCAAACAACTTG Homo sapiens hg19 -STK11_12.chr19.1223059.1223125_tile_1 STK11_12.chr19.1223059.1223125_tile_1 1 chr19 1223035 1223221 + GGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCC Homo sapiens hg19 -JAK3_1.chr19.17945696.17945696_tile_1 JAK3_1.chr19.17945696.17945696_tile_1 1 chr19 17945666 17945840 + GGTGACGCCACTAAACACTTCCCAGACCGTGGCGCCGAAGCCCCACTTGTCAGCTTCCAAGCTAAGTGTCTGCGCCTCCCGGAGACACTCGGGGGCCACCCAGGGGATCCTGTCGGTGAGCAC Homo sapiens hg19 -JAK3_2.chr19.17948009.17948009_tile_1 JAK3_2.chr19.17948009.17948009_tile_1 1 chr19 17947981 17948169 + CGCTGCTTCCAGGAATGACTGGGGAAGGTGGGAAGGGAGAGAAGATGCGTGGGTTTCTTCCACTCCAATAATCCCAAATTTTGTGCTCACAGACCTGCCTTAGGGGAACACCTGGCCACAGGTCACCTTTGGCCCTGG Homo sapiens hg19 -SRC.chr20.36031762.36031762_tile_1 SRC.chr20.36031762.36031762_tile_1 1 chr20 36031734 36031923 + CCAGCCCGGGGAGAACCTCTAGGCACAGGCGGGCCCAGACCGGCTTCTCGGCTTGGATCCTGGGCTGGGTGGCCCCTGTCTCGGGGCTTGCCCCACTCTGCCTGCCTGCTGTTGGTCCTCTCTCTGTGGGGCTGA Homo sapiens hg19 -GNAS1.chr20.57484420.57484421_tile_1 GNAS1.chr20.57484420.57484421_tile_1 1 chr20 57484390 57484560 + TGCCGTGTCCTGACTTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCAGTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCAC Homo sapiens hg19 -SMARCB1_1.chr22.24133967.24133990_tile_1 SMARCB1_1.chr22.24133967.24133990_tile_1 1 chr22 24133939 24134126 + TCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGGAGGCGACTAGCCACTGTGGAAGAGAGGAAGAAAATAGTTGCATCGTCACATGGTAAAAAAACAAAACCTAACACTAAGGGTGCGTCTTCACGAGGGTT Homo sapiens hg19 -SMARCB1_3.chr22.24143240.24143240_tile_1 SMARCB1_3.chr22.24143240.24143240_tile_1 1 chr22 24143210 24143383 + GGGCCGAGACAAGAAGAGAACCTTCCCCCTTTGGTGTGGATGCATCGCTGCACTCACCCTCCGTGCTGATTCCGCCTTAGTTCTCCAGCACGTTTCAGTTCCTTCCTCCCCAGAAAAACACT Homo sapiens hg19 -SMARCB1_4.chr22.24145582.24145582_tile_1 SMARCB1_4.chr22.24145582.24145582_tile_1 1 chr22 24145552 24145726 + GCTGCGAGACGCCTTCACCTGGAACATGAATGGTACAAGGCAGTCGGGCTTGGCTGGGCCTGGCCCCAACCCCTGTGTGTTACGTGGGAACAGTCCCGTTTCCTGCCAGCTGCCTGTCAGGC Homo sapiens hg19 -SMARCB1_5_6.chr22.24176352.24176357_tile_1 SMARCB1_5_6.chr22.24176352.24176357_tile_1 1 chr22 24176324 24176495 + CGGCCCCGGCCTGGTAACCAGCCCATCAGCACACGGCTCCCACGGAGCATCTCAGAAGATTGGGCCGCCTCTCCTCCATCTTCTGGCAAGGACAGAGGCGAGGGGACAGCCCAGCGCCA Homo sapiens hg19 -GNA11_4.chr19.3114942.3115070_tile_1 GNA11_4.chr19.3114942.3115070_tile_1 1 chr19 3114824 3115004 - GTAGCCCAAGGTGGCGATGCGGTCAACGTCGGTCAGGTAGCTGCAACACAGCGGTGGGTGCTCAGGCCGGCTGCCGGGGGTGGGGGGGCAGGACAGGGACACAGCACCCAAACCAGCGGGAGGACGGAAAGCCACC Homo sapiens hg19 -GNA11_4.chr19.3114942.3115070_tile_2 GNA11_4.chr19.3114942.3115070_tile_2 1 chr19 3114958 3115133 + CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCATCATCGAGTACCCTTTCGACCTGGAGAACATCATCTTCCGGTACCGCCCGGGCCACAGCAGGCGGGGAGGGGGCACTGAGA Homo sapiens hg19 -GNA11_5.chr19.3118922.3119051_tile_1 GNA11_5.chr19.3118922.3119051_tile_1 1 chr19 3118802 3118989 - CACTTCCTCCGCTCCGACCGCTGGCCCCCCACATCCACCATCCTGAAAGGACACAGCGCCAGGACTCAGCCACCTGGCGCCCCAAGGCCCAATCTGCAATCCCAGGACGGCTCCCACCCAAGCCCCTCCTGCCACACC Homo sapiens hg19 -GNA11_6.chr19.3119204.3119357_tile_2 GNA11_6.chr19.3119204.3119357_tile_2 1 chr19 3119208 3119395 - CCGCAGCCCGGCGCACCATCGAACTCGGGGAAGTAGTCCACCAGGTGCGAGTACAGGATCTTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGAGGATGACGGAGGAGTTCTGGAACCAGGGGTAGGTGATGATGGTCCGG Homo sapiens hg19 -GNA11_7.chr19.3120987.3121177_tile_1 GNA11_7.chr19.3120987.3121177_tile_1 1 chr19 3120865 3121035 + GGGCCTTACTCGCTCATCCCCTGGGAGTGACAAAGGGGCCCACGAGTCCCTTGCCCTGGGCCGGGCTGGGGCACAGCCTCACCCTCTGCCCTCCCCCAGGTCCCCAGCGGGACGCCCAGGC Homo sapiens hg19 -GNA11_7.chr19.3120987.3121177_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 1 chr19 3120985 3121170 - CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTCCGTGTCGGTGGCACACGTGAAGTGTGAGTAGATGATCTTGTCGCTGTCGGGGTTCAGGTCCACGAACATCTTCAGGATGAACTCCCGCGCCGC Homo sapiens hg19 -GNA11_7.chr19.3120987.3121177_tile_3 GNA11_7.chr19.3120987.3121177_tile_3 1 chr19 3121121 3121304 + GCAGCTCAACCTCAAGGAGTACAACCTGGTCTGAGCGCCCAGGCCCAGGGAGACGGGATGGAGACACGGGGCAGGACCTTCCTTCCACGGAGCCTGCGGCTGCCGGGCGGGTGGCGCTGCCGAGTCCGGGCCGGGGC Homo sapiens hg19 -GNAQ_4.chr9.80412436.80412564_tile_1 GNAQ_4.chr9.80412436.80412564_tile_1 1 chr9 80412406 80412592 + TACCTGAAAATGACACTTTGTAAGTCAAAGGGGTATTCGATGATCCCTGTGGTGGGGACTCGAACTCTAAGCACATCTTGTTGCGTAGGCAGGTAGGCAGGGTCAGCTACGCGGTCCAAGTCATTAAGATAGC Homo sapiens hg19 -GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_5.chr9.80409379.80409508_tile_1 1 chr9 80409249 80409421 + AAAGAAGTAAGTTCACTCCATTCCCCACACCCTACTTTCTATCATTTACTTGTATCAGATAATAAAATGATAATCCATTGCCTGTCTAAAGAACACTTACCTCATTGTCTGACT Homo sapiens hg19 -GNAQ_5.chr9.80409379.80409508_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 1 chr9 80409335 80409510 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCAAGTTCTCGTGGAGTCAGACAATGAGGTAAGTGTTCTTTA Homo sapiens hg19 -GNAQ_5.chr9.80409379.80409508_tile_3 GNAQ_5.chr9.80409379.80409508_tile_3 1 chr9 80409459 80409639 + TTTGGCCCCCTACATCGACCATTCTGCAAGGTTAACAATACTCATATTAATAACATATAAAGTAAAACTAAAAAGTCAACATAAATATAGCACTACTTACAAACTTAGGGAAAATATTCTCTTGAAT Homo sapiens hg19 -GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_6.chr9.80343430.80343583_tile_1 1 chr9 80343306 80343476 + GGGCAGCAATGGTGCACTGTAGTGCGTTAACTCCCACACTGGGGTTTGGAGACAAAACCTATTCACAGCTACTGAGCTGTGGTATGAGTGCTGACTTACCATCATATTCTGGGAAGT Homo sapiens hg19 -GNAQ_6.chr9.80343430.80343583_tile_2 GNAQ_6.chr9.80343430.80343583_tile_2 1 chr9 80343392 80343561 - GGTTCCAGAACTCCTCGGTTATTCTGTTCTTAAACAAGAAAGATCTTCTAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGTAAGTCAGCAC Homo sapiens hg19 -GNAQ_6.chr9.80343430.80343583_tile_3 GNAQ_6.chr9.80343430.80343583_tile_3 1 chr9 80343504 80343689 + CAGGGGTATGTGATAATTGTTCTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTGGAAAAAAAAAAAAAATCAGAAAAAACAAGGAGTGAATTACATGATTACTTAATTTGTGAATTGTGTTTATTTT Homo sapiens hg19 -GNAQ_7.chr9.80336240.80336429_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 1 chr9 80336110 80336280 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCAGGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAATTAGACCAGATTGTACT Homo sapiens hg19 -GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_7.chr9.80336240.80336429_tile_2 1 chr9 80336204 80336374 - CTACTCCCACTTCACGTGCGCCACAGACACCGAGAATATCCGCTTTGTCTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGAGTACAATCTGGTCTAATTGTGCCTCC Homo sapiens hg19 -GNAQ_7.chr9.80336240.80336429_tile_3 GNAQ_7.chr9.80336240.80336429_tile_3 1 chr9 80336320 80336495 + GATAATTTTGTCACTGTCTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCTTTCGGCCAAGAGACAAGAGGGACACTTTGTTACCTA Homo sapiens hg19 -PIK3CA4_11.chr3.178936074.178936095_tile_1 PIK3CA4_11.chr3.178936074.178936095_tile_1 2 chr22 17052964 17053133 + ATCCTCTCTCTGAAATCACTGCGCAGGAGAAAGATTTTCTATGGACCACAGGTAAGTGCTAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGACTTTGG Homo sapiens hg19 -PIK3CA12.chr3.178938860.178938860_tile_1 PIK3CA12.chr3.178938860.178938860_tile_1 2 chr22 17055413 17055585 + CACCTGAATAGGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTGTCAAACAGGAGAAGAAGGATGAAACACAAAAGTTGTGTGACTCTAGTCTGTGTTTGAGACTCTT Homo sapiens hg19 -PTEN7.chr10.89717615.89717772_tile_1 PTEN3.chr10.89685307.89685307_tile_1 2 chr9 33675957 33676480 - ATACACAATCTTTGTGCTGAAAGACATTATGACACCGCCAAATCTAATTACAGAGTTGCGCAATATCCTTTTGAAGACCATAACCCACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTATAATGATTTATGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGGAGTAACTATTCCCAGTCAGAGGCGCTATGTGTATTACTATAGCTACCTGGTAAAGAATCATGTGGATTATAGACCAGTGGCACTGTTGTTTCACAAGATGATGTTTGAAACTATTCCAATGTTCAGTGGCGGAACTTGCAATCCTCAGTTTGTGGTCTGCCAGCTAAAG Homo sapiens hg19 -PTEN13.chr10.89720716.89720852_tile_1 PTEN13.chr10.89720716.89720852_tile_1 2 chr9 33675629 33675815 - CAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATTGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAGTATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACA Homo sapiens hg19 -GNA11_6.chr19.3119204.3119357_tile_2 GNA11_7.chr19.3120987.3121177_tile_2 2 chr7 65970150 65970483 + CAGGATGGTGTCCTTCACGGCCGCGAACACGAAGCGGATGTTCTTCGTGTCGGTGGCGTACGTGAAGTGGGAGTCGATGATCTTGTCGCTGTCGGGGTTCATGTCCACTAACATCTTCAGGATGAACTCCCGCGCCGCCTGGGCGTCCTGCTGGGGCCCTTCGAACTCGGGGAAGTAGTCCACCATGTGTGAGTACAGGATATTGTCCTCCAGCAGGTCCTTCTTGTTGAGGAAGGTGATGACGGGGGAGTTCTGGAACCAGGGGTAGTCGATGATGGTCCGG Homo sapiens hg19 -GNA11_7.chr19.3120987.3121177_tile_1 GNA11_4.chr19.3114942.3115070_tile_2 2 chr7 65970285 65970719 - CCTGCCCACCCAGCAGGACGTGCTGCGGGTCCGCGTGCCCACCACCGGCGTCTTTCGACCTGGAGAACATCATCTTCAGGATGGCGGATGTTGGGGGACAGCGGTCGGCGCAGAGGAAGTGGATCCACTGCTTTGAGAACCTGACGTCCATCCCGTTTCTCGTCGCCCTCAGTGAATACGACCAAGTCCTGGTGGAGTCGGACAACGAGAACCGGATGGAGGAGAGCAAAGCCCTGTTCCGGACCATCATCGACTACCCCTGGTTCCAGAACTCCCCCGTCATCACCTTCCTCAACAAGAAGGACCTGCTGGAGGACAATATCCTGTACTCACACATGGTGGACTACTTCCCCGAGTTCGAAGGGCCCCAGCAGGACGCCCAGGC Homo sapiens hg19 -GNAQ_5.chr9.80409379.80409508_tile_1 GNAQ_7.chr9.80336240.80336429_tile_1 2 chr2 132181238 132181750 + TTAGTATTATGCAAATTGTTTTCCACAGAAATACAGTCCCTCTTGTGTATCTTCAATAGCCCACCATGGAAGGGCAGGGCGGGTGTCTAGGAGGCACAACTAGACCAGATTGTAATCCTTCAGGTTCAACTGGAGGATGGTGTCCTTGACGGCAGCAAACACAAAGCGGATATTCTCGGTGTCTGTGGCGCATGTGAAGTGGGAGTAGATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGTAGTCGACTAGATGGGAATACATGATTTTCTCCTCTGGAAGATCTTTCTTGTTTAACAACAGAATAACCGAGGAGTTCTGGAACCAGGGATACGTGATAATTGTACTAAAGAGAGCCTTGCTTTCCTCCATTCGGTTCTCATTGTCTGACT Homo sapiens hg19 -GNAQ_6.chr9.80343430.80343583_tile_1 GNAQ_7.chr9.80336240.80336429_tile_3 2 chr2 132181448 132181600 + GATAATTTGGTCACTGGGTTCAGGTCCACGAACATCTTCAGAATGAATTCTCGGGCTGCCTGGGCATCTCTCTGGGGTCCATCATATTCTGGGAAGT Homo sapiens hg19 -GNAQ_7.chr9.80336240.80336429_tile_2 GNAQ_5.chr9.80409379.80409508_tile_2 2 chr2 132181332 132181839 - AGGTCAGAGAGAAGAAAATGGATACACTGCTTTGAAAATGTCACCTCTATCATGTTTCTAGTAGCGCTTAGTGAATATGATCGAGTTCTCGTGGAGTCAGACAATGAGAACCGAATGGAGGAAAGCAAGGCTCTCTTTAGTACAATTATCACGTATCCCTGGTTCCAGAACTCCTCGGTTATTCTGTTGTTAAACAAGAAAGATCTTCCAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGACCCCAGAGAGATGCCCAGGCAGCCCGAGAATTCATTCTGAAGATGTTCGTGGACCTGAACCCAGTGACCAAATTATCTACTCCCACTTCACATGCGCCACAGACACCGAGAATATCCGCTTTGTGTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGATTACAATCTGGTCTAGTTGTGCCTCC Homo sapiens hg19
--- a/tool_dependencies.xml Fri Oct 10 11:28:57 2014 -0400 +++ b/tool_dependencies.xml Tue Dec 23 11:26:33 2014 -0500 @@ -1,13 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <!-- PACKAGES --> <package name="R" version="3.1.0"> <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> - <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> @@ -16,30 +15,9 @@ </package> <!-- - <package name="snpeff" version="3.4"> - <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" /> - <readme>Let's see where this msg appears...snpeff</readme> - </package> - <package name="varscan" version="2"> - <repository name="varscan_version_2" owner="devteam" prior_installation_required="TRUE" /> - <readme>Let's see where this msg appears...varscan</readme> - </package> - --> - - <!-- ENV --> - <set_environment> <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - <!-- - <set_environment> - <environment_variable action="set_to" name="JAR_PATH1">$JAVA_JAR_PATH</environment_variable> - </set_environment> - <set_environment> - <environment_variable action="set_to" name="JAR_PATH2">$SNPEFF_JAR_PATH</environment_variable> - </set_environment> --> - - <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>--> </tool_dependency>