Mercurial > repos > devteam > samtools_stats
changeset 1:cc56fc603e53 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:56:27 -0400 |
| parents | cd6eb75c9819 |
| children | b02596e3d7a3 |
| files | macros.xml samtools_stats.xml test-data/samtools_stats_input.bam test-data/samtools_stats_out1.tab test-data/samtools_stats_out2.tab test-data/samtools_stats_out2/cov.tab test-data/samtools_stats_out2/gcc.tab test-data/samtools_stats_out2/gcd.tab test-data/samtools_stats_out2/gcf.tab test-data/samtools_stats_out2/gcl.tab test-data/samtools_stats_out2/mpc.tab test-data/samtools_stats_out2/sn.tab test-data/samtools_stats_ref.fa tool_dependencies.xml |
| diffstat | 14 files changed, 3190 insertions(+), 2077 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 13 12:56:27 2015 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros>
--- a/samtools_stats.xml Mon Oct 20 14:56:49 2014 -0400 +++ b/samtools_stats.xml Tue Oct 13 12:56:27 2015 -0400 @@ -1,9 +1,11 @@ -<tool id="samtools_stats" name="Generate statistics" version="1.0.0"> - <description>for a BAM or SAM file</description> - <requirements> - <requirement type="package" version="1.1">samtools</requirement> - </requirements> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> +<tool id="samtools_stats" name="Stats" version="2.0"> + <description>generate statistics for BAM dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> <command><![CDATA[ #if $use_reference.use_ref_selector == "yes": #if $use_reference.reference_source.reference_source_selector == "history": @@ -27,6 +29,14 @@ #end if --GC-depth ${gc_depth} --insert-size ${insert_size} + + ## The code below is commented out because using -I/--id options causes the following exception + ## Samtools-htslib: init_group_id() header parsing not yet implemented + + ##if str($read_group) != "": + ## -I "${read_group}" + ##end if + #if str($read_length) != "0": --read-length "${read_length}" #end if @@ -43,60 +53,88 @@ #if $split_output.split_output_selector == "yes": #set outputs_to_split = str($split_output.generate_tables).split(',') && mkdir split && echo ${split_output.generate_tables} && + #if 'sn' in $outputs_to_split: - grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- > "split/Summary numbers.tab" ; fi && + echo "# Summary Numbers\n" > "split/Summary numbers.tab" && + grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi && #end if + #if 'ffq' in $outputs_to_split: - grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- > "split/First Fragment Qualities.tab" ; fi && + echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" && + grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi && #end if + #if 'lfq' in $outputs_to_split: - grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- > "split/Last Fragment Qualities.tab" ; fi && + echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" && + grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi && #end if + #if 'mpc' in $outputs_to_split: - grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- > "split/Mismatches per cycle.tab" ; fi && + echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" && + grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi && #end if + #if 'gcf' in $outputs_to_split: - grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- > "split/GC Content of first fragments.tab" ; fi && + echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" && + grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi && #end if + #if 'gcl' in $outputs_to_split: - grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- > "split/GC Content of last fragments.tab" ; fi && + echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" && + grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi && #end if + #if 'gcc' in $outputs_to_split: - grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- > "split/ACGT content per cycle.tab" ; fi && + echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" && + grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi && #end if + #if 'is' in $outputs_to_split: - grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- > "split/Insert sizes.tab" ; fi && + echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" && + grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- >> "split/Insert sizes.tab" ; fi && #end if + #if 'rl' in $outputs_to_split: - grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- > "split/Read lengths.tab" ; fi && + echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" && + grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- >> "split/Read lengths.tab" ; fi && #end if + #if 'id' in $outputs_to_split: - grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- > "split/Indel distribution.tab" ; fi && + echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" && + grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- >> "split/Indel distribution.tab" ; fi && #end if + #if 'ic' in $outputs_to_split: - grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- > "split/Indels per cycle.tab" ; fi && + echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" && + grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- >> "split/Indels per cycle.tab" ; fi && #end if + #if 'cov' in $outputs_to_split: - grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- > "split/Coverage distribution.tab" ; fi && + echo "# Coverage distribution" > "split/Coverage distribution.tab" && + grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi && #end if + #if 'gcd' in $outputs_to_split: - grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- > "split/GC depth.tab" ; fi + echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" && + grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi && #end if + + ## Unix true command below + + true + #end if ]]></command> - <stdio> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> <inputs> <param name="input_file" type="data" format="sam,bam" label="BAM file" /> - <param name="coverage_min" type="integer" value="1" label="Minimum coverage" /> - <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" /> - <param name="coverage_step" type="integer" value="1" label="Coverage step" /> - <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" /> + <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/> + <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/> + <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/> + <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/> <conditional name="split_output"> - <param name="split_output_selector" type="select" label="Output"> - <option value="no" selected="True">Output to a summary file</option> - <option value="yes">Extract separate statistics</option> + <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics"> + <option value="no" selected="True">a single summary file</option> + <option value="yes">separate datasets for each statistics</option> </param> <when value="no" /> <when value="yes"> @@ -118,12 +156,12 @@ </when> </conditional> <conditional name="filter_by_flags"> - <param name="filter_flags" type="select" label="Set filter by flags"> + <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options"> <option value="nofilter" selected="True">Do not filter</option> <option value="filter">Filter by flags to exclude or require</option> </param> <when value="filter"> - <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require"> + <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f"> <option value="1">Read is paired</option> <option value="2">Read is mapped in a proper pair</option> <option value="4">The read is unmapped</option> @@ -136,7 +174,7 @@ <option value="512">The read fails platform/vendor quality checks</option> <option value="1024">The read is a PCR or optical duplicate</option> </param> - <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude"> + <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F"> <option value="1">Read is paired</option> <option value="2">Read is mapped in a proper pair</option> <option value="4">The read is unmapped</option> @@ -151,17 +189,36 @@ </param> </when> <when value="nofilter" /> + </conditional> - <param name="gc_depth" type="float" value="2000" label="GC-depth bin size" /> - <param name="insert_size" type="integer" value="8000" label="Maximum insert size" /> - <param name="read_group" type="text" optional="true" label="Limit to a specific read group name" /> - <param name="read_length" type="integer" value="0" optional="true" label="Minimum read length to generate statistics for" /> - <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" /> - <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" /> + <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/> + <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/> + + <!-- + + The -I option of samtools stats returns the following message in version 1.2: + + Samtools-htslib: init_group_id() header parsing not yet implemented + Abort trap: 6 + + Because of this the section below is commented out until this stats bug is fixed + + <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > + <options> + <filter type="data_meta" ref="input_file" key="read_groups" /> + </options> + </param> + + --> + + <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/> + <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/> + <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/> + <conditional name="use_reference"> - <param name="use_ref_selector" type="select" label="Use reference sequence"> + <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation"> <option value="yes">Use reference</option> - <option value="no">Do not use reference</option> + <option selected="True" value="no">Do not use reference</option> </param> <when value="yes"> <conditional name="reference_source"> @@ -182,7 +239,9 @@ </when> <when value="no" /> </conditional> + </inputs> + <outputs> <data format="tabular" name="output" label="${tool.name} on ${on_string}"> <discover_datasets pattern="(?P<designation>.+)\.tab" ext="tabular" visible="true" directory="split" /> @@ -190,38 +249,48 @@ </outputs> <tests> <test> - <param name="input_file" value="phiX.bam" ftype="bam" /> - <param name="use_ref_selector" value="no" /> - <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" /> + <param name="input_file" value="samtools_stats_input.bam" ftype="bam" /> + <param name="use_ref_selector" value="yes" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> + <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" /> </test> <test> - <param name="input_file" value="phiX.bam" ftype="bam" /> - <param name="use_ref_selector" value="no" /> + <param name="input_file" value="samtools_stats_input.bam" ftype="bam" /> + <param name="use_ref_selector" value="yes" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> <param name="split_output_selector" value="yes" /> - <param name="generate_tables" value="sn,gcf,gcl,gcc,cov,gcd" /> - <output name="output" file="samtools_stats_out2.tab" lines_diff="2"> + <param name="generate_tables" value="sn,mpc,gcc" /> + <output name="output" file="samtools_stats_out2.tab" lines_diff="4"> <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" /> - <discovered_dataset designation="GC Content of first fragments" ftype="tabular" file="samtools_stats_out2/gcf.tab" /> - <discovered_dataset designation="GC Content of last fragments" ftype="tabular" file="samtools_stats_out2/gcl.tab" /> <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" /> - <discovered_dataset designation="Coverage distribution" ftype="tabular" file="samtools_stats_out2/cov.tab" /> - <discovered_dataset designation="GC depth" ftype="tabular" file="samtools_stats_out2/gcd.tab" /> + <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" /> </output> </test> </tests> - <help> + <help><![CDATA[ **What it does** -This tool runs the ``samtools stats`` command in the SAMtools toolkit. - -Collects statistics from BAM files. The output can be visualized using plot-bamstats. - -**Citation** +This tool runs the ``samtools stats`` command. It has the following options:: -For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ - + -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1] + -d, --remove-dups Exclude from statistics reads marked as duplicates + -f, --required-flag <str|int> Required flag, 0 for unset. See also `samtools flags` [0] + -F, --filtering-flag <str|int> Filtering flag, 0 for unset. See also `samtools flags` [0] + --GC-depth <float> the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4] + -h, --help This help message + -i, --insert-size <int> Maximum insert size [8000] + -I, --id <string> Include only listed read group or sample name + -l, --read-length <int> Include in the statistics only reads with the given read length [] + -m, --most-inserts <float> Report only the main part of inserts [0.99] + -q, --trim-quality <int> The BWA trimming parameter [0] + -r, --ref-seq <file> Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy + will provide options for selecting a reference cached as this Galaxy instance or choosing + one from history. + -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - </help> + ]]></help> + <expand macro="citations"></expand> </tool>
--- a/test-data/samtools_stats_out1.tab Mon Oct 20 14:56:49 2014 -0400 +++ b/test-data/samtools_stats_out1.tab Tue Oct 13 12:56:27 2015 -0400 @@ -1,951 +1,1137 @@ -# This file was produced by samtools stats (1.1+htslib-1.1) and can be plotted using plot-bamstats -# The command line was: stats --coverage 1,1000,1 --GC-depth 2000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 /tmp/tmptYfjRJ/tmpl0qHNN/database/files/000/dataset_929.dat +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) -CHK 76594422 342222f2 06e86208 +CHK 1bd20fd8 58ad2167 29883386 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 1000 +SN raw total sequences: 200 SN filtered sequences: 0 -SN sequences: 1000 +SN sequences: 200 SN is sorted: 1 -SN 1st fragments: 500 -SN last fragments: 500 -SN reads mapped: 972 -SN reads mapped and paired: 954 # paired-end technology bit set + both mates mapped -SN reads unmapped: 28 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 SN reads properly paired: 0 # proper-pair bit set -SN reads paired: 1000 # paired-end technology bit set +SN reads paired: 200 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set -SN reads MQ0: 0 # mapped and MQ=0 +SN reads MQ0: 6 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 -SN total length: 70000 # ignores clipping -SN bases mapped: 68040 # ignores clipping -SN bases mapped (cigar): 68040 # more accurate +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate SN bases trimmed: 0 SN bases duplicated: 0 -SN mismatches: 1237 # from NM fields -SN error rate: 1.818048e-02 # mismatches / bases mapped (cigar) -SN average length: 70 -SN maximum length: 70 -SN average quality: 17.0 -SN insert size average: 495.1 -SN insert size standard deviation: 48.9 -SN inward oriented pairs: 477 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 0 # First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to cycles. 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Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. -GCF 14.82 0 -GCF 31.16 2 -GCF 33.42 6 -GCF 34.92 4 -GCF 36.18 6 -GCF 37.44 12 -GCF 38.94 28 -GCF 40.45 34 -GCF 41.96 37 -GCF 43.47 46 -GCF 44.72 55 -GCF 45.98 57 -GCF 47.49 68 -GCF 48.99 60 -GCF 50.50 27 -GCF 52.01 18 -GCF 53.52 15 -GCF 54.77 9 -GCF 56.03 4 -GCF 57.54 3 -GCF 59.05 2 -GCF 60.55 4 -GCF 62.06 0 -GCF 63.32 1 +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. -GCL 14.07 0 -GCL 28.89 1 -GCL 30.40 3 -GCL 31.91 1 -GCL 33.42 2 -GCL 34.92 4 -GCL 36.18 8 -GCL 37.44 16 -GCL 38.94 31 -GCL 40.45 40 -GCL 41.96 39 -GCL 43.47 55 -GCL 44.72 46 -GCL 45.98 61 -GCL 47.49 53 -GCL 48.99 50 -GCL 50.50 32 -GCL 52.01 23 -GCL 53.52 11 -GCL 54.77 9 -GCL 56.03 8 -GCL 57.54 3 -GCL 61.06 1 +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 # ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] -GCC 1 21.50 23.30 24.50 30.70 -GCC 2 21.10 22.20 22.50 34.20 -GCC 3 22.20 20.50 26.80 30.50 -GCC 4 24.40 21.50 21.50 32.60 -GCC 5 23.50 21.10 25.60 29.80 -GCC 6 26.30 21.80 20.40 31.50 -GCC 7 25.40 20.50 22.00 32.10 -GCC 8 23.90 19.20 27.00 29.90 -GCC 9 23.70 22.70 22.00 31.60 -GCC 10 22.50 22.00 24.10 31.40 -GCC 11 22.40 21.50 22.10 34.00 -GCC 12 25.20 18.00 24.50 32.30 -GCC 13 23.70 20.80 21.70 33.80 -GCC 14 24.60 23.00 22.40 30.00 -GCC 15 25.50 22.30 22.50 29.70 -GCC 16 24.10 21.40 23.60 30.90 -GCC 17 24.30 21.00 23.90 30.80 -GCC 18 24.40 22.10 22.70 30.80 -GCC 19 25.60 20.50 24.70 29.20 -GCC 20 25.80 19.60 22.00 32.60 -GCC 21 23.20 22.90 23.00 30.90 -GCC 22 23.90 22.70 22.60 30.80 -GCC 23 25.80 21.30 22.40 30.50 -GCC 24 23.50 22.00 22.70 31.80 -GCC 25 22.40 21.80 23.10 32.70 -GCC 26 22.90 19.90 24.30 32.90 -GCC 27 23.10 22.10 24.20 30.60 -GCC 28 23.50 22.10 22.90 31.50 -GCC 29 24.40 21.80 21.30 32.50 -GCC 30 21.90 22.50 22.60 33.00 -GCC 31 23.10 20.90 24.20 31.80 -GCC 32 24.60 22.10 23.60 29.70 -GCC 33 22.80 21.10 22.00 34.10 -GCC 34 21.70 22.10 23.60 32.60 -GCC 35 24.30 23.20 20.60 31.90 -GCC 36 21.60 22.70 24.50 31.20 -GCC 37 22.20 23.50 22.20 32.10 -GCC 38 24.10 20.80 22.00 33.10 -GCC 39 22.20 21.10 26.80 29.90 -GCC 40 21.80 24.00 22.90 31.30 -GCC 41 25.10 22.90 23.10 28.90 -GCC 42 25.50 22.70 22.20 29.60 -GCC 43 22.60 23.00 24.10 30.30 -GCC 44 21.70 21.60 24.20 32.50 -GCC 45 21.80 22.70 21.20 34.30 -GCC 46 22.80 22.00 23.80 31.40 -GCC 47 23.70 22.30 23.90 30.10 -GCC 48 24.30 21.70 24.80 29.20 -GCC 49 23.90 22.00 22.90 31.20 -GCC 50 23.50 22.40 22.80 31.30 -GCC 51 23.30 20.40 24.70 31.60 -GCC 52 23.30 20.20 25.10 31.40 -GCC 53 23.70 22.00 22.30 32.00 -GCC 54 23.30 21.30 25.40 30.00 -GCC 55 25.30 21.40 22.60 30.70 -GCC 56 24.40 24.10 19.20 32.30 -GCC 57 22.00 21.50 24.50 32.00 -GCC 58 24.90 21.20 24.20 29.70 -GCC 59 24.10 21.70 24.50 29.70 -GCC 60 24.80 20.90 25.10 29.20 -GCC 61 21.30 21.60 28.10 29.00 -GCC 62 23.80 21.80 21.70 32.70 -GCC 63 23.30 22.80 23.50 30.40 -GCC 64 24.00 21.40 23.50 31.10 -GCC 65 24.40 22.80 22.50 30.30 -GCC 66 24.70 22.30 21.40 31.60 -GCC 67 22.40 21.10 24.60 31.90 -GCC 68 24.60 22.90 20.60 31.90 -GCC 69 22.40 23.00 23.10 31.50 -GCC 70 23.50 19.50 23.90 33.10 -# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs -IS 0 0 0 0 0 -IS 1 0 0 0 0 -IS 2 0 0 0 0 -IS 3 0 0 0 0 -IS 4 0 0 0 0 -IS 5 0 0 0 0 -IS 6 0 0 0 0 -IS 7 0 0 0 0 -IS 8 0 0 0 0 -IS 9 0 0 0 0 -IS 10 0 0 0 0 -IS 11 0 0 0 0 -IS 12 0 0 0 0 -IS 13 0 0 0 0 -IS 14 0 0 0 0 -IS 15 0 0 0 0 -IS 16 0 0 0 0 -IS 17 0 0 0 0 -IS 18 0 0 0 0 -IS 19 0 0 0 0 -IS 20 0 0 0 0 -IS 21 0 0 0 0 -IS 22 0 0 0 0 -IS 23 0 0 0 0 -IS 24 0 0 0 0 -IS 25 0 0 0 0 -IS 26 0 0 0 0 -IS 27 0 0 0 0 -IS 28 0 0 0 0 -IS 29 0 0 0 0 -IS 30 0 0 0 0 -IS 31 0 0 0 0 -IS 32 0 0 0 0 -IS 33 0 0 0 0 -IS 34 0 0 0 0 -IS 35 0 0 0 0 -IS 36 0 0 0 0 -IS 37 0 0 0 0 -IS 38 0 0 0 0 -IS 39 0 0 0 0 -IS 40 0 0 0 0 -IS 41 0 0 0 0 -IS 42 0 0 0 0 -IS 43 0 0 0 0 -IS 44 0 0 0 0 -IS 45 0 0 0 0 -IS 46 0 0 0 0 -IS 47 0 0 0 0 -IS 48 0 0 0 0 -IS 49 0 0 0 0 -IS 50 0 0 0 0 -IS 51 0 0 0 0 -IS 52 0 0 0 0 -IS 53 0 0 0 0 -IS 54 0 0 0 0 -IS 55 0 0 0 0 -IS 56 0 0 0 0 -IS 57 0 0 0 0 -IS 58 0 0 0 0 -IS 59 0 0 0 0 -IS 60 0 0 0 0 -IS 61 0 0 0 0 -IS 62 0 0 0 0 -IS 63 0 0 0 0 -IS 64 0 0 0 0 -IS 65 0 0 0 0 -IS 66 0 0 0 0 -IS 67 0 0 0 0 -IS 68 0 0 0 0 -IS 69 0 0 0 0 -IS 70 0 0 0 0 -IS 71 0 0 0 0 -IS 72 0 0 0 0 -IS 73 0 0 0 0 -IS 74 0 0 0 0 -IS 75 0 0 0 0 -IS 76 0 0 0 0 -IS 77 0 0 0 0 -IS 78 0 0 0 0 -IS 79 0 0 0 0 -IS 80 0 0 0 0 -IS 81 0 0 0 0 -IS 82 0 0 0 0 -IS 83 0 0 0 0 -IS 84 0 0 0 0 -IS 85 0 0 0 0 -IS 86 0 0 0 0 -IS 87 0 0 0 0 -IS 88 0 0 0 0 -IS 89 0 0 0 0 -IS 90 0 0 0 0 -IS 91 0 0 0 0 -IS 92 0 0 0 0 -IS 93 0 0 0 0 -IS 94 0 0 0 0 -IS 95 0 0 0 0 -IS 96 0 0 0 0 -IS 97 0 0 0 0 -IS 98 0 0 0 0 -IS 99 0 0 0 0 -IS 100 0 0 0 0 -IS 101 0 0 0 0 -IS 102 0 0 0 0 -IS 103 0 0 0 0 -IS 104 0 0 0 0 -IS 105 0 0 0 0 -IS 106 0 0 0 0 -IS 107 0 0 0 0 -IS 108 0 0 0 0 -IS 109 0 0 0 0 -IS 110 0 0 0 0 -IS 111 0 0 0 0 -IS 112 0 0 0 0 -IS 113 0 0 0 0 -IS 114 0 0 0 0 -IS 115 0 0 0 0 -IS 116 0 0 0 0 -IS 117 0 0 0 0 -IS 118 0 0 0 0 -IS 119 0 0 0 0 -IS 120 0 0 0 0 -IS 121 0 0 0 0 -IS 122 0 0 0 0 -IS 123 0 0 0 0 -IS 124 0 0 0 0 -IS 125 0 0 0 0 -IS 126 0 0 0 0 -IS 127 0 0 0 0 -IS 128 0 0 0 0 -IS 129 0 0 0 0 -IS 130 0 0 0 0 -IS 131 0 0 0 0 -IS 132 0 0 0 0 -IS 133 0 0 0 0 -IS 134 0 0 0 0 -IS 135 0 0 0 0 -IS 136 0 0 0 0 -IS 137 0 0 0 0 -IS 138 0 0 0 0 -IS 139 0 0 0 0 -IS 140 0 0 0 0 -IS 141 0 0 0 0 -IS 142 0 0 0 0 -IS 143 0 0 0 0 -IS 144 0 0 0 0 -IS 145 0 0 0 0 -IS 146 0 0 0 0 -IS 147 0 0 0 0 -IS 148 0 0 0 0 -IS 149 0 0 0 0 -IS 150 0 0 0 0 -IS 151 0 0 0 0 -IS 152 0 0 0 0 -IS 153 0 0 0 0 -IS 154 0 0 0 0 -IS 155 0 0 0 0 -IS 156 0 0 0 0 -IS 157 0 0 0 0 -IS 158 0 0 0 0 -IS 159 0 0 0 0 -IS 160 0 0 0 0 -IS 161 0 0 0 0 -IS 162 0 0 0 0 -IS 163 0 0 0 0 -IS 164 0 0 0 0 -IS 165 0 0 0 0 -IS 166 0 0 0 0 -IS 167 0 0 0 0 -IS 168 0 0 0 0 -IS 169 0 0 0 0 -IS 170 0 0 0 0 -IS 171 0 0 0 0 -IS 172 0 0 0 0 -IS 173 0 0 0 0 -IS 174 0 0 0 0 -IS 175 0 0 0 0 -IS 176 0 0 0 0 -IS 177 0 0 0 0 -IS 178 0 0 0 0 -IS 179 0 0 0 0 -IS 180 0 0 0 0 -IS 181 0 0 0 0 -IS 182 0 0 0 0 -IS 183 0 0 0 0 -IS 184 0 0 0 0 -IS 185 0 0 0 0 -IS 186 0 0 0 0 -IS 187 0 0 0 0 -IS 188 0 0 0 0 -IS 189 0 0 0 0 -IS 190 0 0 0 0 -IS 191 0 0 0 0 -IS 192 0 0 0 0 -IS 193 0 0 0 0 -IS 194 0 0 0 0 -IS 195 0 0 0 0 -IS 196 0 0 0 0 -IS 197 0 0 0 0 -IS 198 0 0 0 0 -IS 199 0 0 0 0 -IS 200 0 0 0 0 -IS 201 0 0 0 0 -IS 202 0 0 0 0 -IS 203 0 0 0 0 -IS 204 0 0 0 0 -IS 205 0 0 0 0 -IS 206 0 0 0 0 -IS 207 0 0 0 0 -IS 208 0 0 0 0 -IS 209 0 0 0 0 -IS 210 0 0 0 0 -IS 211 0 0 0 0 -IS 212 0 0 0 0 -IS 213 0 0 0 0 -IS 214 0 0 0 0 -IS 215 0 0 0 0 -IS 216 0 0 0 0 -IS 217 0 0 0 0 -IS 218 0 0 0 0 -IS 219 0 0 0 0 -IS 220 0 0 0 0 -IS 221 0 0 0 0 -IS 222 0 0 0 0 -IS 223 0 0 0 0 -IS 224 0 0 0 0 -IS 225 0 0 0 0 -IS 226 0 0 0 0 -IS 227 0 0 0 0 -IS 228 0 0 0 0 -IS 229 0 0 0 0 -IS 230 0 0 0 0 -IS 231 0 0 0 0 -IS 232 0 0 0 0 -IS 233 0 0 0 0 -IS 234 0 0 0 0 -IS 235 0 0 0 0 -IS 236 0 0 0 0 -IS 237 0 0 0 0 -IS 238 0 0 0 0 -IS 239 0 0 0 0 -IS 240 0 0 0 0 -IS 241 0 0 0 0 -IS 242 0 0 0 0 -IS 243 0 0 0 0 -IS 244 0 0 0 0 -IS 245 0 0 0 0 -IS 246 0 0 0 0 -IS 247 0 0 0 0 -IS 248 0 0 0 0 -IS 249 0 0 0 0 -IS 250 0 0 0 0 -IS 251 0 0 0 0 -IS 252 0 0 0 0 -IS 253 0 0 0 0 -IS 254 0 0 0 0 -IS 255 0 0 0 0 -IS 256 0 0 0 0 -IS 257 0 0 0 0 -IS 258 0 0 0 0 -IS 259 0 0 0 0 -IS 260 0 0 0 0 -IS 261 0 0 0 0 -IS 262 0 0 0 0 -IS 263 0 0 0 0 -IS 264 0 0 0 0 -IS 265 0 0 0 0 -IS 266 0 0 0 0 -IS 267 0 0 0 0 -IS 268 0 0 0 0 -IS 269 0 0 0 0 -IS 270 0 0 0 0 -IS 271 0 0 0 0 -IS 272 0 0 0 0 -IS 273 0 0 0 0 -IS 274 0 0 0 0 -IS 275 0 0 0 0 -IS 276 0 0 0 0 -IS 277 0 0 0 0 -IS 278 0 0 0 0 -IS 279 0 0 0 0 -IS 280 0 0 0 0 -IS 281 0 0 0 0 -IS 282 0 0 0 0 -IS 283 0 0 0 0 -IS 284 0 0 0 0 -IS 285 0 0 0 0 -IS 286 0 0 0 0 -IS 287 0 0 0 0 -IS 288 0 0 0 0 -IS 289 0 0 0 0 -IS 290 0 0 0 0 -IS 291 0 0 0 0 -IS 292 0 0 0 0 -IS 293 0 0 0 0 -IS 294 0 0 0 0 -IS 295 0 0 0 0 -IS 296 0 0 0 0 -IS 297 0 0 0 0 -IS 298 0 0 0 0 -IS 299 0 0 0 0 -IS 300 0 0 0 0 -IS 301 0 0 0 0 -IS 302 0 0 0 0 -IS 303 0 0 0 0 -IS 304 0 0 0 0 -IS 305 0 0 0 0 -IS 306 0 0 0 0 -IS 307 0 0 0 0 -IS 308 0 0 0 0 -IS 309 0 0 0 0 -IS 310 0 0 0 0 -IS 311 1 1 0 0 -IS 312 0 0 0 0 -IS 313 0 0 0 0 -IS 314 0 0 0 0 -IS 315 0 0 0 0 -IS 316 0 0 0 0 -IS 317 0 0 0 0 -IS 318 0 0 0 0 -IS 319 0 0 0 0 -IS 320 0 0 0 0 -IS 321 0 0 0 0 -IS 322 0 0 0 0 -IS 323 0 0 0 0 -IS 324 0 0 0 0 -IS 325 0 0 0 0 -IS 326 0 0 0 0 -IS 327 0 0 0 0 -IS 328 0 0 0 0 -IS 329 0 0 0 0 -IS 330 0 0 0 0 -IS 331 0 0 0 0 -IS 332 0 0 0 0 -IS 333 0 0 0 0 -IS 334 0 0 0 0 -IS 335 0 0 0 0 -IS 336 0 0 0 0 -IS 337 0 0 0 0 -IS 338 0 0 0 0 -IS 339 0 0 0 0 -IS 340 0 0 0 0 -IS 341 0 0 0 0 -IS 342 0 0 0 0 -IS 343 0 0 0 0 -IS 344 0 0 0 0 -IS 345 1 1 0 0 -IS 346 0 0 0 0 -IS 347 1 1 0 0 -IS 348 0 0 0 0 -IS 349 0 0 0 0 -IS 350 0 0 0 0 -IS 351 0 0 0 0 -IS 352 0 0 0 0 -IS 353 0 0 0 0 -IS 354 0 0 0 0 -IS 355 0 0 0 0 -IS 356 0 0 0 0 -IS 357 0 0 0 0 -IS 358 0 0 0 0 -IS 359 0 0 0 0 -IS 360 0 0 0 0 -IS 361 0 0 0 0 -IS 362 0 0 0 0 -IS 363 0 0 0 0 -IS 364 1 1 0 0 -IS 365 0 0 0 0 -IS 366 0 0 0 0 -IS 367 0 0 0 0 -IS 368 0 0 0 0 -IS 369 0 0 0 0 -IS 370 1 1 0 0 -IS 371 1 1 0 0 -IS 372 0 0 0 0 -IS 373 0 0 0 0 -IS 374 0 0 0 0 -IS 375 0 0 0 0 -IS 376 0 0 0 0 -IS 377 0 0 0 0 -IS 378 2 2 0 0 -IS 379 0 0 0 0 -IS 380 0 0 0 0 -IS 381 0 0 0 0 -IS 382 0 0 0 0 -IS 383 0 0 0 0 -IS 384 0 0 0 0 -IS 385 0 0 0 0 -IS 386 0 0 0 0 -IS 387 1 1 0 0 -IS 388 1 1 0 0 -IS 389 0 0 0 0 -IS 390 1 1 0 0 -IS 391 0 0 0 0 -IS 392 0 0 0 0 -IS 393 0 0 0 0 -IS 394 1 1 0 0 -IS 395 1 1 0 0 -IS 396 1 1 0 0 -IS 397 0 0 0 0 -IS 398 1 1 0 0 -IS 399 0 0 0 0 -IS 400 1 1 0 0 -IS 401 0 0 0 0 -IS 402 0 0 0 0 -IS 403 1 1 0 0 -IS 404 0 0 0 0 -IS 405 0 0 0 0 -IS 406 0 0 0 0 -IS 407 1 1 0 0 -IS 408 1 1 0 0 -IS 409 3 3 0 0 -IS 410 4 4 0 0 -IS 411 0 0 0 0 -IS 412 0 0 0 0 -IS 413 1 1 0 0 -IS 414 1 1 0 0 -IS 415 1 1 0 0 -IS 416 1 1 0 0 -IS 417 0 0 0 0 -IS 418 1 1 0 0 -IS 419 0 0 0 0 -IS 420 1 1 0 0 -IS 421 1 1 0 0 -IS 422 0 0 0 0 -IS 423 0 0 0 0 -IS 424 3 3 0 0 -IS 425 3 3 0 0 -IS 426 0 0 0 0 -IS 427 1 1 0 0 -IS 428 1 1 0 0 -IS 429 0 0 0 0 -IS 430 0 0 0 0 -IS 431 4 4 0 0 -IS 432 1 1 0 0 -IS 433 1 1 0 0 -IS 434 3 3 0 0 -IS 435 1 1 0 0 -IS 436 1 1 0 0 -IS 437 0 0 0 0 -IS 438 1 1 0 0 -IS 439 0 0 0 0 -IS 440 3 3 0 0 -IS 441 1 1 0 0 -IS 442 4 4 0 0 -IS 443 3 3 0 0 -IS 444 1 1 0 0 -IS 445 4 4 0 0 -IS 446 1 1 0 0 -IS 447 1 1 0 0 -IS 448 1 1 0 0 -IS 449 2 2 0 0 -IS 450 3 3 0 0 -IS 451 5 5 0 0 -IS 452 2 2 0 0 -IS 453 3 3 0 0 -IS 454 4 4 0 0 -IS 455 7 7 0 0 -IS 456 3 3 0 0 -IS 457 4 4 0 0 -IS 458 2 2 0 0 -IS 459 3 3 0 0 -IS 460 2 2 0 0 -IS 461 2 2 0 0 -IS 462 2 2 0 0 -IS 463 2 2 0 0 -IS 464 1 1 0 0 -IS 465 6 6 0 0 -IS 466 4 4 0 0 -IS 467 6 6 0 0 -IS 468 1 1 0 0 -IS 469 1 1 0 0 -IS 470 1 1 0 0 -IS 471 3 3 0 0 -IS 472 8 8 0 0 -IS 473 4 4 0 0 -IS 474 2 2 0 0 -IS 475 2 2 0 0 -IS 476 4 4 0 0 -IS 477 6 6 0 0 -IS 478 3 3 0 0 -IS 479 6 6 0 0 -IS 480 7 7 0 0 -IS 481 3 3 0 0 -IS 482 2 2 0 0 -IS 483 1 1 0 0 -IS 484 6 6 0 0 -IS 485 6 6 0 0 -IS 486 6 6 0 0 -IS 487 2 2 0 0 -IS 488 4 4 0 0 -IS 489 3 3 0 0 -IS 490 6 6 0 0 -IS 491 3 3 0 0 -IS 492 5 5 0 0 -IS 493 2 2 0 0 -IS 494 4 4 0 0 -IS 495 0 0 0 0 -IS 496 7 7 0 0 -IS 497 5 5 0 0 -IS 498 4 4 0 0 -IS 499 6 6 0 0 -IS 500 0 0 0 0 -IS 501 2 2 0 0 -IS 502 2 2 0 0 -IS 503 4 4 0 0 -IS 504 3 3 0 0 -IS 505 3 3 0 0 -IS 506 2 2 0 0 -IS 507 4 4 0 0 -IS 508 3 3 0 0 -IS 509 1 1 0 0 -IS 510 7 7 0 0 -IS 511 2 2 0 0 -IS 512 3 3 0 0 -IS 513 7 7 0 0 -IS 514 4 4 0 0 -IS 515 2 2 0 0 -IS 516 2 2 0 0 -IS 517 1 1 0 0 -IS 518 0 0 0 0 -IS 519 2 2 0 0 -IS 520 2 2 0 0 -IS 521 5 5 0 0 -IS 522 6 6 0 0 -IS 523 4 4 0 0 -IS 524 2 2 0 0 -IS 525 1 1 0 0 -IS 526 5 5 0 0 -IS 527 6 6 0 0 -IS 528 0 0 0 0 -IS 529 5 5 0 0 -IS 530 7 7 0 0 -IS 531 4 4 0 0 -IS 532 5 5 0 0 -IS 533 1 1 0 0 -IS 534 5 5 0 0 -IS 535 3 3 0 0 -IS 536 2 2 0 0 -IS 537 3 3 0 0 -IS 538 2 2 0 0 -IS 539 4 4 0 0 -IS 540 2 2 0 0 -IS 541 2 2 0 0 -IS 542 3 3 0 0 -IS 543 4 4 0 0 -IS 544 2 2 0 0 -IS 545 1 1 0 0 -IS 546 2 2 0 0 -IS 547 2 2 0 0 -IS 548 3 3 0 0 -IS 549 5 5 0 0 -IS 550 1 1 0 0 -IS 551 0 0 0 0 -IS 552 0 0 0 0 -IS 553 4 4 0 0 -IS 554 1 1 0 0 -IS 555 5 5 0 0 -IS 556 5 5 0 0 -IS 557 2 2 0 0 -IS 558 2 2 0 0 -IS 559 3 3 0 0 -IS 560 1 1 0 0 -IS 561 1 1 0 0 -IS 562 4 4 0 0 -IS 563 1 1 0 0 -IS 564 1 1 0 0 -IS 565 0 0 0 0 -IS 566 1 1 0 0 -IS 567 1 1 0 0 -IS 568 0 0 0 0 -IS 569 2 2 0 0 -IS 570 1 1 0 0 -IS 571 2 2 0 0 -IS 572 4 4 0 0 -IS 573 0 0 0 0 -IS 574 0 0 0 0 -IS 575 0 0 0 0 -IS 576 1 1 0 0 -IS 577 2 2 0 0 -IS 578 1 1 0 0 -IS 579 2 2 0 0 -IS 580 0 0 0 0 -IS 581 1 1 0 0 -IS 582 0 0 0 0 -IS 583 1 1 0 0 -IS 584 2 2 0 0 -IS 585 0 0 0 0 -IS 586 3 3 0 0 -IS 587 0 0 0 0 -IS 588 0 0 0 0 -IS 589 0 0 0 0 -IS 590 0 0 0 0 -IS 591 0 0 0 0 -IS 592 0 0 0 0 -IS 593 0 0 0 0 -IS 594 2 2 0 0 -IS 595 0 0 0 0 -IS 596 0 0 0 0 -IS 597 1 1 0 0 -IS 598 0 0 0 0 -IS 599 0 0 0 0 -IS 600 1 1 0 0 -IS 601 1 1 0 0 -IS 602 0 0 0 0 -IS 603 0 0 0 0 -IS 604 0 0 0 0 -IS 605 1 1 0 0 -IS 606 0 0 0 0 -IS 607 1 1 0 0 -IS 608 0 0 0 0 -IS 609 0 0 0 0 -IS 610 0 0 0 0 -IS 611 1 1 0 0 +GCC 1 21.50 29.50 33.50 15.50 +GCC 2 30.00 16.00 11.00 43.00 +GCC 3 33.00 25.00 9.00 33.00 +GCC 4 17.00 29.00 13.00 41.00 +GCC 5 37.00 22.00 12.00 29.00 +GCC 6 36.00 26.00 17.00 21.00 +GCC 7 29.50 13.50 31.50 25.50 +GCC 8 50.50 14.50 19.50 15.50 +GCC 9 17.00 33.00 18.00 32.00 +GCC 10 37.00 14.00 21.00 28.00 +GCC 11 20.50 14.50 29.50 35.50 +GCC 12 30.00 24.00 22.00 24.00 +GCC 13 27.00 15.00 21.00 37.00 +GCC 14 24.00 22.00 26.00 28.00 +GCC 15 25.50 20.50 24.50 29.50 +GCC 16 31.00 15.00 20.00 34.00 +GCC 17 28.00 25.00 14.00 33.00 +GCC 18 30.50 28.50 19.50 21.50 +GCC 19 29.00 26.00 21.00 24.00 +GCC 20 22.50 23.50 17.50 36.50 +GCC 21 35.50 17.50 19.50 27.50 +GCC 22 37.50 28.50 15.50 18.50 +GCC 23 31.00 19.00 13.00 37.00 +GCC 24 37.00 12.00 22.00 29.00 +GCC 25 35.50 22.50 17.50 24.50 +GCC 26 33.50 18.50 15.50 32.50 +GCC 27 34.50 14.50 25.50 25.50 +GCC 28 31.00 14.00 24.00 31.00 +GCC 29 30.00 27.00 24.00 19.00 +GCC 30 31.00 20.00 14.00 35.00 +GCC 31 33.50 29.50 13.50 23.50 +GCC 32 42.50 20.50 19.50 17.50 +GCC 33 25.50 23.50 14.50 36.50 +GCC 34 39.50 16.50 20.50 23.50 +GCC 35 32.50 23.50 21.50 22.50 +GCC 36 42.00 25.00 16.00 17.00 +GCC 37 38.00 17.00 19.00 26.00 +GCC 38 24.00 26.00 25.00 25.00 +GCC 39 22.50 41.50 18.50 17.50 +GCC 40 32.00 16.00 21.00 31.00 +GCC 41 33.00 28.00 19.00 20.00 +GCC 42 30.50 25.50 19.50 24.50 +GCC 43 35.00 29.00 15.00 21.00 +GCC 44 20.00 27.00 22.00 31.00 +GCC 45 40.50 21.50 21.50 16.50 +GCC 46 26.50 20.50 22.50 30.50 +GCC 47 38.50 29.50 16.50 15.50 +GCC 48 27.50 24.50 17.50 30.50 +GCC 49 28.50 32.50 10.50 28.50 +GCC 50 46.50 20.50 9.50 23.50 +GCC 51 34.50 28.50 13.50 23.50 +GCC 52 41.50 23.50 20.50 14.50 +GCC 53 20.00 28.00 26.00 26.00 +GCC 54 31.50 18.50 24.50 25.50 +GCC 55 30.50 22.50 16.50 30.50 +GCC 56 33.50 22.50 13.50 30.50 +GCC 57 23.00 24.00 23.00 30.00 +GCC 58 25.00 37.00 19.00 19.00 +GCC 59 34.00 23.00 24.00 19.00 +GCC 60 29.00 28.00 17.00 26.00 +GCC 61 25.50 23.50 24.50 26.50 +GCC 62 31.50 22.50 16.50 29.50 +GCC 63 27.50 28.50 25.50 18.50 +GCC 64 33.50 21.50 25.50 19.50 +GCC 65 35.50 19.50 18.50 26.50 +GCC 66 34.00 25.00 15.00 26.00 +GCC 67 37.00 23.00 19.00 21.00 +GCC 68 36.50 29.50 13.50 20.50 +GCC 69 38.50 19.50 20.50 21.50 +GCC 70 38.50 16.50 18.50 26.50 +GCC 71 25.50 38.50 21.50 14.50 +GCC 72 29.00 29.00 25.00 17.00 +GCC 73 32.50 20.50 21.50 25.50 +GCC 74 28.50 32.50 12.50 26.50 +GCC 75 41.50 12.50 18.50 27.50 +GCC 76 24.50 29.50 23.50 22.50 +GCC 77 36.00 21.00 18.00 25.00 +GCC 78 27.00 34.00 22.00 17.00 +GCC 79 21.50 26.50 25.50 26.50 +GCC 80 34.00 19.00 28.00 19.00 +GCC 81 17.00 26.00 26.00 31.00 +GCC 82 31.00 30.00 23.00 16.00 +GCC 83 31.50 26.50 12.50 29.50 +GCC 84 19.00 41.00 21.00 19.00 +GCC 85 37.50 24.50 16.50 21.50 +GCC 86 15.00 48.00 15.00 22.00 +GCC 87 41.00 16.00 18.00 25.00 +GCC 88 23.50 27.50 27.50 21.50 +GCC 89 26.50 27.50 26.50 19.50 +GCC 90 18.50 23.50 24.50 33.50 +GCC 91 27.00 32.00 22.00 19.00 +GCC 92 23.50 17.50 27.50 31.50 +GCC 93 25.50 37.50 15.50 21.50 +GCC 94 27.00 17.00 24.00 32.00 +GCC 95 26.50 37.50 14.50 21.50 +GCC 96 29.50 25.50 16.50 28.50 +GCC 97 29.00 31.00 21.00 19.00 +GCC 98 18.00 33.00 22.00 27.00 +GCC 99 24.50 33.50 24.50 17.50 +GCC 100 24.50 16.50 24.50 34.50 +GCC 101 25.00 40.00 19.00 16.00 +GCC 102 17.50 17.50 32.50 32.50 +GCC 103 31.00 26.00 16.00 27.00 +GCC 104 26.50 29.50 20.50 23.50 +GCC 105 34.00 33.00 21.00 12.00 +GCC 106 23.00 31.00 26.00 20.00 +GCC 107 17.50 35.50 23.50 23.50 +GCC 108 24.50 30.50 23.50 21.50 +GCC 109 17.00 31.00 22.00 30.00 +GCC 110 16.00 35.00 24.00 25.00 +GCC 111 24.00 32.00 23.00 21.00 +GCC 112 37.00 28.00 16.00 19.00 +GCC 113 19.50 22.50 32.50 25.50 +GCC 114 17.00 31.00 35.00 17.00 +GCC 115 29.50 24.50 23.50 22.50 +GCC 116 22.00 30.00 34.00 14.00 +GCC 117 27.00 23.00 19.00 31.00 +GCC 118 25.50 14.50 34.50 25.50 +GCC 119 22.50 34.50 20.50 22.50 +GCC 120 17.50 24.50 26.50 31.50 +GCC 121 27.50 33.50 22.50 16.50 +GCC 122 17.00 23.00 25.00 35.00 +GCC 123 23.50 46.50 11.50 18.50 +GCC 124 9.00 32.00 34.00 25.00 +GCC 125 24.00 27.00 19.00 30.00 +GCC 126 26.00 17.00 28.00 29.00 +GCC 127 26.50 16.50 21.50 35.50 +GCC 128 18.00 34.00 31.00 17.00 +GCC 129 25.50 25.50 27.50 21.50 +GCC 130 25.00 20.00 22.00 33.00 +GCC 131 17.50 39.50 24.50 18.50 +GCC 132 21.00 28.00 23.00 28.00 +GCC 133 13.50 31.50 35.50 19.50 +GCC 134 24.50 19.50 30.50 25.50 +GCC 135 16.50 23.50 30.50 29.50 +GCC 136 28.00 32.00 15.00 25.00 +GCC 137 22.50 21.50 30.50 25.50 +GCC 138 14.50 34.50 24.50 26.50 +GCC 139 20.50 29.50 24.50 25.50 +GCC 140 17.00 23.00 30.00 30.00 +GCC 141 20.50 23.50 25.50 30.50 +GCC 142 18.00 29.00 38.00 15.00 +GCC 143 22.00 24.00 27.00 27.00 +GCC 144 21.50 30.50 26.50 21.50 +GCC 145 22.00 21.00 29.00 28.00 +GCC 146 25.00 16.00 39.00 20.00 +GCC 147 26.50 22.50 30.50 20.50 +GCC 148 12.50 28.50 36.50 22.50 +GCC 149 26.50 23.50 23.50 26.50 +GCC 150 14.00 29.00 24.00 33.00 +GCC 151 19.50 30.50 32.50 17.50 +GCC 152 18.50 17.50 29.50 34.50 +GCC 153 22.50 22.50 31.50 23.50 +GCC 154 22.00 21.00 29.00 28.00 +GCC 155 21.00 26.00 19.00 34.00 +GCC 156 14.50 23.50 35.50 26.50 +GCC 157 22.00 31.00 23.00 24.00 +GCC 158 22.50 29.50 24.50 23.50 +GCC 159 17.50 12.50 46.50 23.50 +GCC 160 24.50 26.50 26.50 22.50 +GCC 161 13.00 23.00 45.00 19.00 +GCC 162 31.50 16.50 22.50 29.50 +GCC 163 19.50 21.50 35.50 23.50 +GCC 164 29.00 18.00 21.00 32.00 +GCC 165 14.50 17.50 35.50 32.50 +GCC 166 17.50 37.50 28.50 16.50 +GCC 167 16.50 21.50 31.50 30.50 +GCC 168 14.00 25.00 30.00 31.00 +GCC 169 18.50 20.50 23.50 37.50 +GCC 170 19.00 23.00 28.00 30.00 +GCC 171 20.00 28.00 33.00 19.00 +GCC 172 19.00 20.00 32.00 29.00 +GCC 173 24.50 16.50 33.50 25.50 +GCC 174 17.50 23.50 33.50 25.50 +GCC 175 33.50 17.50 35.50 13.50 +GCC 176 16.50 32.50 28.50 22.50 +GCC 177 19.00 22.00 27.00 32.00 +GCC 178 16.00 26.00 30.00 28.00 +GCC 179 18.00 18.00 22.00 42.00 +GCC 180 21.00 22.00 34.00 23.00 +GCC 181 20.50 19.50 35.50 24.50 +GCC 182 32.50 18.50 22.50 26.50 +GCC 183 24.50 13.50 28.50 33.50 +GCC 184 15.00 29.00 30.00 26.00 +GCC 185 15.00 32.00 33.00 20.00 +GCC 186 22.50 23.50 34.50 19.50 +GCC 187 19.00 14.00 40.00 27.00 +GCC 188 27.50 21.50 27.50 23.50 +GCC 189 17.00 22.00 34.00 27.00 +GCC 190 23.00 30.00 23.00 24.00 +GCC 191 25.00 22.00 28.00 25.00 +GCC 192 34.50 24.50 13.50 27.50 +GCC 193 18.50 25.50 25.50 30.50 +GCC 194 18.50 33.50 24.50 23.50 +GCC 195 16.00 26.00 23.00 35.00 +GCC 196 21.50 25.50 24.50 28.50 +GCC 197 20.00 21.00 23.00 36.00 +GCC 198 17.00 21.00 37.00 25.00 +GCC 199 20.50 18.50 25.50 35.50 +GCC 200 21.00 29.00 21.00 29.00 +GCC 201 27.00 21.00 23.00 29.00 +GCC 202 21.50 24.50 19.50 34.50 +GCC 203 21.50 24.50 26.50 27.50 +GCC 204 27.00 29.00 24.00 20.00 +GCC 205 19.50 21.50 22.50 36.50 +GCC 206 26.50 24.50 21.50 27.50 +GCC 207 22.50 21.50 19.50 36.50 +GCC 208 14.00 35.00 29.00 22.00 +GCC 209 16.00 23.00 12.00 49.00 +GCC 210 18.50 19.50 40.50 21.50 +GCC 211 26.00 20.00 22.00 32.00 +GCC 212 21.00 31.00 18.00 30.00 +GCC 213 24.00 15.00 31.00 30.00 +GCC 214 17.50 24.50 25.50 32.50 +GCC 215 26.00 24.00 23.00 27.00 +GCC 216 21.50 17.50 25.50 35.50 +GCC 217 26.00 29.00 17.00 28.00 +GCC 218 20.00 27.00 21.00 32.00 +GCC 219 17.00 21.00 21.00 41.00 +GCC 220 25.50 23.50 23.50 27.50 +GCC 221 21.50 23.50 20.50 34.50 +GCC 222 21.50 21.50 18.50 38.50 +GCC 223 20.00 27.00 28.00 25.00 +GCC 224 22.50 22.50 24.50 30.50 +GCC 225 14.50 35.50 30.50 19.50 +GCC 226 20.00 23.00 26.00 31.00 +GCC 227 20.50 24.50 23.50 31.50 +GCC 228 33.00 19.00 26.00 22.00 +GCC 229 22.50 24.50 18.50 34.50 +GCC 230 21.00 32.00 16.00 31.00 +GCC 231 23.00 28.00 30.00 19.00 +GCC 232 23.50 21.50 12.50 42.50 +GCC 233 21.00 27.00 25.00 27.00 +GCC 234 16.50 27.50 22.50 33.50 +GCC 235 20.00 15.00 28.00 37.00 +GCC 236 28.00 23.00 21.00 28.00 +GCC 237 20.50 19.50 22.50 37.50 +GCC 238 21.50 29.50 24.50 24.50 +GCC 239 20.00 8.00 17.00 55.00 +GCC 240 28.00 24.00 16.00 32.00 +GCC 241 22.50 22.50 16.50 38.50 +GCC 242 29.00 25.00 13.00 33.00 +GCC 243 22.50 15.50 23.50 38.50 +GCC 244 20.50 23.50 16.50 39.50 +GCC 245 28.00 23.00 19.00 30.00 +GCC 246 21.00 29.00 25.00 25.00 +GCC 247 32.00 14.00 13.00 41.00 +GCC 248 18.00 18.00 25.00 39.00 +GCC 249 25.00 23.00 21.00 31.00 +GCC 250 27.50 22.50 17.50 32.50 +GCC 251 13.50 20.50 36.50 29.50 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count -RL 70 1000 +RL 251 200 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions -ID 1 0 1 +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 # Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) -IC 8 0 0 1 0 +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. -COV [1-1] 1 42 -COV [2-2] 2 59 -COV [3-3] 3 73 -COV [4-4] 4 98 -COV [5-5] 5 128 -COV [6-6] 6 142 -COV [7-7] 7 226 -COV [8-8] 8 241 -COV [9-9] 9 281 -COV [10-10] 10 400 -COV [11-11] 11 450 -COV [12-12] 12 444 -COV [13-13] 13 433 -COV [14-14] 14 423 -COV [15-15] 15 392 -COV [16-16] 16 434 -COV [17-17] 17 294 -COV [18-18] 18 229 -COV [19-19] 19 143 -COV [20-20] 20 143 -COV [21-21] 21 149 -COV [22-22] 22 90 -COV [23-23] 23 41 -COV [24-24] 24 14 +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile -GCD 0.0 50.000 0.000 0.000 0.000 0.000 0.000 -GCD 44.0 75.000 14.875 14.875 14.875 14.875 14.875 -GCD 46.0 100.000 11.900 11.900 11.900 11.900 11.900 +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000
--- a/test-data/samtools_stats_out2.tab Mon Oct 20 14:56:49 2014 -0400 +++ b/test-data/samtools_stats_out2.tab Tue Oct 13 12:56:27 2015 -0400 @@ -1,951 +1,1137 @@ -# This file was produced by samtools stats (1.1+htslib-1.1) and can be plotted using plot-bamstats -# The command line was: stats --coverage 1,1000,1 --GC-depth 2000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 /tmp/tmpFDCqQD/tmprMv9KZ/database/files/000/dataset_893.dat +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) -CHK 76594422 342222f2 06e86208 +CHK 1bd20fd8 58ad2167 29883386 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. -SN raw total sequences: 1000 +SN raw total sequences: 200 SN filtered sequences: 0 -SN sequences: 1000 +SN sequences: 200 SN is sorted: 1 -SN 1st fragments: 500 -SN last fragments: 500 -SN reads mapped: 972 -SN reads mapped and paired: 954 # paired-end technology bit set + both mates mapped -SN reads unmapped: 28 +SN 1st fragments: 100 +SN last fragments: 100 +SN reads mapped: 25 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 175 SN reads properly paired: 0 # proper-pair bit set -SN reads paired: 1000 # paired-end technology bit set +SN reads paired: 200 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set -SN reads MQ0: 0 # mapped and MQ=0 +SN reads MQ0: 6 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 -SN total length: 70000 # ignores clipping -SN bases mapped: 68040 # ignores clipping -SN bases mapped (cigar): 68040 # more accurate +SN total length: 50200 # ignores clipping +SN bases mapped: 6275 # ignores clipping +SN bases mapped (cigar): 6275 # more accurate SN bases trimmed: 0 SN bases duplicated: 0 -SN mismatches: 1237 # from NM fields -SN error rate: 1.818048e-02 # mismatches / bases mapped (cigar) -SN average length: 70 -SN maximum length: 70 -SN average quality: 17.0 -SN insert size average: 495.1 -SN insert size standard deviation: 48.9 -SN inward oriented pairs: 477 +SN mismatches: 591 # from NM fields +SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +SN average length: 251 +SN maximum length: 251 +SN average quality: 34.7 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 0 # First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to cycles. First column is the cycle number. -FFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -FFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. First column is the cycle number, second +# is the number of N's and the rest is the number of mismatches +MPC 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +MPC 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 +MPC 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 +MPC 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +MPC 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 +MPC 184 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 185 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 186 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 187 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 188 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 189 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 190 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 191 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 192 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 193 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 195 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 196 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 197 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 198 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 199 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 203 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 204 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 205 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 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0 0 +MPC 227 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 228 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 229 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 230 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 231 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 232 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +MPC 233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 234 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 235 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 236 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 237 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 238 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 239 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 240 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 241 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 242 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +MPC 243 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 244 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 245 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 246 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 247 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 +MPC 248 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 3 2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +MPC 249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +MPC 250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +MPC 251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +MPC 252 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. -GCF 14.82 0 -GCF 31.16 2 -GCF 33.42 6 -GCF 34.92 4 -GCF 36.18 6 -GCF 37.44 12 -GCF 38.94 28 -GCF 40.45 34 -GCF 41.96 37 -GCF 43.47 46 -GCF 44.72 55 -GCF 45.98 57 -GCF 47.49 68 -GCF 48.99 60 -GCF 50.50 27 -GCF 52.01 18 -GCF 53.52 15 -GCF 54.77 9 -GCF 56.03 4 -GCF 57.54 3 -GCF 59.05 2 -GCF 60.55 4 -GCF 62.06 0 -GCF 63.32 1 +GCF 21.86 0 +GCF 44.22 2 +GCF 44.97 8 +GCF 45.48 4 +GCF 45.98 3 +GCF 46.48 5 +GCF 46.98 2 +GCF 47.49 3 +GCF 47.99 12 +GCF 48.49 13 +GCF 48.99 9 +GCF 49.50 2 +GCF 50.25 3 +GCF 51.01 6 +GCF 51.51 4 +GCF 52.01 1 +GCF 52.51 0 +GCF 53.02 1 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. -GCL 14.07 0 -GCL 28.89 1 -GCL 30.40 3 -GCL 31.91 1 -GCL 33.42 2 -GCL 34.92 4 -GCL 36.18 8 -GCL 37.44 16 -GCL 38.94 31 -GCL 40.45 40 -GCL 41.96 39 -GCL 43.47 55 -GCL 44.72 46 -GCL 45.98 61 -GCL 47.49 53 -GCL 48.99 50 -GCL 50.50 32 -GCL 52.01 23 -GCL 53.52 11 -GCL 54.77 9 -GCL 56.03 8 -GCL 57.54 3 -GCL 61.06 1 +GCL 21.86 0 +GCL 44.22 2 +GCL 44.97 8 +GCL 45.48 4 +GCL 45.98 3 +GCL 46.48 5 +GCL 46.98 2 +GCL 47.49 3 +GCL 47.99 12 +GCL 48.49 13 +GCL 48.99 9 +GCL 49.50 2 +GCL 50.25 3 +GCL 51.01 6 +GCL 51.51 4 +GCL 52.01 1 +GCL 52.51 0 +GCL 53.02 1 # ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] -GCC 1 21.50 23.30 24.50 30.70 -GCC 2 21.10 22.20 22.50 34.20 -GCC 3 22.20 20.50 26.80 30.50 -GCC 4 24.40 21.50 21.50 32.60 -GCC 5 23.50 21.10 25.60 29.80 -GCC 6 26.30 21.80 20.40 31.50 -GCC 7 25.40 20.50 22.00 32.10 -GCC 8 23.90 19.20 27.00 29.90 -GCC 9 23.70 22.70 22.00 31.60 -GCC 10 22.50 22.00 24.10 31.40 -GCC 11 22.40 21.50 22.10 34.00 -GCC 12 25.20 18.00 24.50 32.30 -GCC 13 23.70 20.80 21.70 33.80 -GCC 14 24.60 23.00 22.40 30.00 -GCC 15 25.50 22.30 22.50 29.70 -GCC 16 24.10 21.40 23.60 30.90 -GCC 17 24.30 21.00 23.90 30.80 -GCC 18 24.40 22.10 22.70 30.80 -GCC 19 25.60 20.50 24.70 29.20 -GCC 20 25.80 19.60 22.00 32.60 -GCC 21 23.20 22.90 23.00 30.90 -GCC 22 23.90 22.70 22.60 30.80 -GCC 23 25.80 21.30 22.40 30.50 -GCC 24 23.50 22.00 22.70 31.80 -GCC 25 22.40 21.80 23.10 32.70 -GCC 26 22.90 19.90 24.30 32.90 -GCC 27 23.10 22.10 24.20 30.60 -GCC 28 23.50 22.10 22.90 31.50 -GCC 29 24.40 21.80 21.30 32.50 -GCC 30 21.90 22.50 22.60 33.00 -GCC 31 23.10 20.90 24.20 31.80 -GCC 32 24.60 22.10 23.60 29.70 -GCC 33 22.80 21.10 22.00 34.10 -GCC 34 21.70 22.10 23.60 32.60 -GCC 35 24.30 23.20 20.60 31.90 -GCC 36 21.60 22.70 24.50 31.20 -GCC 37 22.20 23.50 22.20 32.10 -GCC 38 24.10 20.80 22.00 33.10 -GCC 39 22.20 21.10 26.80 29.90 -GCC 40 21.80 24.00 22.90 31.30 -GCC 41 25.10 22.90 23.10 28.90 -GCC 42 25.50 22.70 22.20 29.60 -GCC 43 22.60 23.00 24.10 30.30 -GCC 44 21.70 21.60 24.20 32.50 -GCC 45 21.80 22.70 21.20 34.30 -GCC 46 22.80 22.00 23.80 31.40 -GCC 47 23.70 22.30 23.90 30.10 -GCC 48 24.30 21.70 24.80 29.20 -GCC 49 23.90 22.00 22.90 31.20 -GCC 50 23.50 22.40 22.80 31.30 -GCC 51 23.30 20.40 24.70 31.60 -GCC 52 23.30 20.20 25.10 31.40 -GCC 53 23.70 22.00 22.30 32.00 -GCC 54 23.30 21.30 25.40 30.00 -GCC 55 25.30 21.40 22.60 30.70 -GCC 56 24.40 24.10 19.20 32.30 -GCC 57 22.00 21.50 24.50 32.00 -GCC 58 24.90 21.20 24.20 29.70 -GCC 59 24.10 21.70 24.50 29.70 -GCC 60 24.80 20.90 25.10 29.20 -GCC 61 21.30 21.60 28.10 29.00 -GCC 62 23.80 21.80 21.70 32.70 -GCC 63 23.30 22.80 23.50 30.40 -GCC 64 24.00 21.40 23.50 31.10 -GCC 65 24.40 22.80 22.50 30.30 -GCC 66 24.70 22.30 21.40 31.60 -GCC 67 22.40 21.10 24.60 31.90 -GCC 68 24.60 22.90 20.60 31.90 -GCC 69 22.40 23.00 23.10 31.50 -GCC 70 23.50 19.50 23.90 33.10 -# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs -IS 0 0 0 0 0 -IS 1 0 0 0 0 -IS 2 0 0 0 0 -IS 3 0 0 0 0 -IS 4 0 0 0 0 -IS 5 0 0 0 0 -IS 6 0 0 0 0 -IS 7 0 0 0 0 -IS 8 0 0 0 0 -IS 9 0 0 0 0 -IS 10 0 0 0 0 -IS 11 0 0 0 0 -IS 12 0 0 0 0 -IS 13 0 0 0 0 -IS 14 0 0 0 0 -IS 15 0 0 0 0 -IS 16 0 0 0 0 -IS 17 0 0 0 0 -IS 18 0 0 0 0 -IS 19 0 0 0 0 -IS 20 0 0 0 0 -IS 21 0 0 0 0 -IS 22 0 0 0 0 -IS 23 0 0 0 0 -IS 24 0 0 0 0 -IS 25 0 0 0 0 -IS 26 0 0 0 0 -IS 27 0 0 0 0 -IS 28 0 0 0 0 -IS 29 0 0 0 0 -IS 30 0 0 0 0 -IS 31 0 0 0 0 -IS 32 0 0 0 0 -IS 33 0 0 0 0 -IS 34 0 0 0 0 -IS 35 0 0 0 0 -IS 36 0 0 0 0 -IS 37 0 0 0 0 -IS 38 0 0 0 0 -IS 39 0 0 0 0 -IS 40 0 0 0 0 -IS 41 0 0 0 0 -IS 42 0 0 0 0 -IS 43 0 0 0 0 -IS 44 0 0 0 0 -IS 45 0 0 0 0 -IS 46 0 0 0 0 -IS 47 0 0 0 0 -IS 48 0 0 0 0 -IS 49 0 0 0 0 -IS 50 0 0 0 0 -IS 51 0 0 0 0 -IS 52 0 0 0 0 -IS 53 0 0 0 0 -IS 54 0 0 0 0 -IS 55 0 0 0 0 -IS 56 0 0 0 0 -IS 57 0 0 0 0 -IS 58 0 0 0 0 -IS 59 0 0 0 0 -IS 60 0 0 0 0 -IS 61 0 0 0 0 -IS 62 0 0 0 0 -IS 63 0 0 0 0 -IS 64 0 0 0 0 -IS 65 0 0 0 0 -IS 66 0 0 0 0 -IS 67 0 0 0 0 -IS 68 0 0 0 0 -IS 69 0 0 0 0 -IS 70 0 0 0 0 -IS 71 0 0 0 0 -IS 72 0 0 0 0 -IS 73 0 0 0 0 -IS 74 0 0 0 0 -IS 75 0 0 0 0 -IS 76 0 0 0 0 -IS 77 0 0 0 0 -IS 78 0 0 0 0 -IS 79 0 0 0 0 -IS 80 0 0 0 0 -IS 81 0 0 0 0 -IS 82 0 0 0 0 -IS 83 0 0 0 0 -IS 84 0 0 0 0 -IS 85 0 0 0 0 -IS 86 0 0 0 0 -IS 87 0 0 0 0 -IS 88 0 0 0 0 -IS 89 0 0 0 0 -IS 90 0 0 0 0 -IS 91 0 0 0 0 -IS 92 0 0 0 0 -IS 93 0 0 0 0 -IS 94 0 0 0 0 -IS 95 0 0 0 0 -IS 96 0 0 0 0 -IS 97 0 0 0 0 -IS 98 0 0 0 0 -IS 99 0 0 0 0 -IS 100 0 0 0 0 -IS 101 0 0 0 0 -IS 102 0 0 0 0 -IS 103 0 0 0 0 -IS 104 0 0 0 0 -IS 105 0 0 0 0 -IS 106 0 0 0 0 -IS 107 0 0 0 0 -IS 108 0 0 0 0 -IS 109 0 0 0 0 -IS 110 0 0 0 0 -IS 111 0 0 0 0 -IS 112 0 0 0 0 -IS 113 0 0 0 0 -IS 114 0 0 0 0 -IS 115 0 0 0 0 -IS 116 0 0 0 0 -IS 117 0 0 0 0 -IS 118 0 0 0 0 -IS 119 0 0 0 0 -IS 120 0 0 0 0 -IS 121 0 0 0 0 -IS 122 0 0 0 0 -IS 123 0 0 0 0 -IS 124 0 0 0 0 -IS 125 0 0 0 0 -IS 126 0 0 0 0 -IS 127 0 0 0 0 -IS 128 0 0 0 0 -IS 129 0 0 0 0 -IS 130 0 0 0 0 -IS 131 0 0 0 0 -IS 132 0 0 0 0 -IS 133 0 0 0 0 -IS 134 0 0 0 0 -IS 135 0 0 0 0 -IS 136 0 0 0 0 -IS 137 0 0 0 0 -IS 138 0 0 0 0 -IS 139 0 0 0 0 -IS 140 0 0 0 0 -IS 141 0 0 0 0 -IS 142 0 0 0 0 -IS 143 0 0 0 0 -IS 144 0 0 0 0 -IS 145 0 0 0 0 -IS 146 0 0 0 0 -IS 147 0 0 0 0 -IS 148 0 0 0 0 -IS 149 0 0 0 0 -IS 150 0 0 0 0 -IS 151 0 0 0 0 -IS 152 0 0 0 0 -IS 153 0 0 0 0 -IS 154 0 0 0 0 -IS 155 0 0 0 0 -IS 156 0 0 0 0 -IS 157 0 0 0 0 -IS 158 0 0 0 0 -IS 159 0 0 0 0 -IS 160 0 0 0 0 -IS 161 0 0 0 0 -IS 162 0 0 0 0 -IS 163 0 0 0 0 -IS 164 0 0 0 0 -IS 165 0 0 0 0 -IS 166 0 0 0 0 -IS 167 0 0 0 0 -IS 168 0 0 0 0 -IS 169 0 0 0 0 -IS 170 0 0 0 0 -IS 171 0 0 0 0 -IS 172 0 0 0 0 -IS 173 0 0 0 0 -IS 174 0 0 0 0 -IS 175 0 0 0 0 -IS 176 0 0 0 0 -IS 177 0 0 0 0 -IS 178 0 0 0 0 -IS 179 0 0 0 0 -IS 180 0 0 0 0 -IS 181 0 0 0 0 -IS 182 0 0 0 0 -IS 183 0 0 0 0 -IS 184 0 0 0 0 -IS 185 0 0 0 0 -IS 186 0 0 0 0 -IS 187 0 0 0 0 -IS 188 0 0 0 0 -IS 189 0 0 0 0 -IS 190 0 0 0 0 -IS 191 0 0 0 0 -IS 192 0 0 0 0 -IS 193 0 0 0 0 -IS 194 0 0 0 0 -IS 195 0 0 0 0 -IS 196 0 0 0 0 -IS 197 0 0 0 0 -IS 198 0 0 0 0 -IS 199 0 0 0 0 -IS 200 0 0 0 0 -IS 201 0 0 0 0 -IS 202 0 0 0 0 -IS 203 0 0 0 0 -IS 204 0 0 0 0 -IS 205 0 0 0 0 -IS 206 0 0 0 0 -IS 207 0 0 0 0 -IS 208 0 0 0 0 -IS 209 0 0 0 0 -IS 210 0 0 0 0 -IS 211 0 0 0 0 -IS 212 0 0 0 0 -IS 213 0 0 0 0 -IS 214 0 0 0 0 -IS 215 0 0 0 0 -IS 216 0 0 0 0 -IS 217 0 0 0 0 -IS 218 0 0 0 0 -IS 219 0 0 0 0 -IS 220 0 0 0 0 -IS 221 0 0 0 0 -IS 222 0 0 0 0 -IS 223 0 0 0 0 -IS 224 0 0 0 0 -IS 225 0 0 0 0 -IS 226 0 0 0 0 -IS 227 0 0 0 0 -IS 228 0 0 0 0 -IS 229 0 0 0 0 -IS 230 0 0 0 0 -IS 231 0 0 0 0 -IS 232 0 0 0 0 -IS 233 0 0 0 0 -IS 234 0 0 0 0 -IS 235 0 0 0 0 -IS 236 0 0 0 0 -IS 237 0 0 0 0 -IS 238 0 0 0 0 -IS 239 0 0 0 0 -IS 240 0 0 0 0 -IS 241 0 0 0 0 -IS 242 0 0 0 0 -IS 243 0 0 0 0 -IS 244 0 0 0 0 -IS 245 0 0 0 0 -IS 246 0 0 0 0 -IS 247 0 0 0 0 -IS 248 0 0 0 0 -IS 249 0 0 0 0 -IS 250 0 0 0 0 -IS 251 0 0 0 0 -IS 252 0 0 0 0 -IS 253 0 0 0 0 -IS 254 0 0 0 0 -IS 255 0 0 0 0 -IS 256 0 0 0 0 -IS 257 0 0 0 0 -IS 258 0 0 0 0 -IS 259 0 0 0 0 -IS 260 0 0 0 0 -IS 261 0 0 0 0 -IS 262 0 0 0 0 -IS 263 0 0 0 0 -IS 264 0 0 0 0 -IS 265 0 0 0 0 -IS 266 0 0 0 0 -IS 267 0 0 0 0 -IS 268 0 0 0 0 -IS 269 0 0 0 0 -IS 270 0 0 0 0 -IS 271 0 0 0 0 -IS 272 0 0 0 0 -IS 273 0 0 0 0 -IS 274 0 0 0 0 -IS 275 0 0 0 0 -IS 276 0 0 0 0 -IS 277 0 0 0 0 -IS 278 0 0 0 0 -IS 279 0 0 0 0 -IS 280 0 0 0 0 -IS 281 0 0 0 0 -IS 282 0 0 0 0 -IS 283 0 0 0 0 -IS 284 0 0 0 0 -IS 285 0 0 0 0 -IS 286 0 0 0 0 -IS 287 0 0 0 0 -IS 288 0 0 0 0 -IS 289 0 0 0 0 -IS 290 0 0 0 0 -IS 291 0 0 0 0 -IS 292 0 0 0 0 -IS 293 0 0 0 0 -IS 294 0 0 0 0 -IS 295 0 0 0 0 -IS 296 0 0 0 0 -IS 297 0 0 0 0 -IS 298 0 0 0 0 -IS 299 0 0 0 0 -IS 300 0 0 0 0 -IS 301 0 0 0 0 -IS 302 0 0 0 0 -IS 303 0 0 0 0 -IS 304 0 0 0 0 -IS 305 0 0 0 0 -IS 306 0 0 0 0 -IS 307 0 0 0 0 -IS 308 0 0 0 0 -IS 309 0 0 0 0 -IS 310 0 0 0 0 -IS 311 1 1 0 0 -IS 312 0 0 0 0 -IS 313 0 0 0 0 -IS 314 0 0 0 0 -IS 315 0 0 0 0 -IS 316 0 0 0 0 -IS 317 0 0 0 0 -IS 318 0 0 0 0 -IS 319 0 0 0 0 -IS 320 0 0 0 0 -IS 321 0 0 0 0 -IS 322 0 0 0 0 -IS 323 0 0 0 0 -IS 324 0 0 0 0 -IS 325 0 0 0 0 -IS 326 0 0 0 0 -IS 327 0 0 0 0 -IS 328 0 0 0 0 -IS 329 0 0 0 0 -IS 330 0 0 0 0 -IS 331 0 0 0 0 -IS 332 0 0 0 0 -IS 333 0 0 0 0 -IS 334 0 0 0 0 -IS 335 0 0 0 0 -IS 336 0 0 0 0 -IS 337 0 0 0 0 -IS 338 0 0 0 0 -IS 339 0 0 0 0 -IS 340 0 0 0 0 -IS 341 0 0 0 0 -IS 342 0 0 0 0 -IS 343 0 0 0 0 -IS 344 0 0 0 0 -IS 345 1 1 0 0 -IS 346 0 0 0 0 -IS 347 1 1 0 0 -IS 348 0 0 0 0 -IS 349 0 0 0 0 -IS 350 0 0 0 0 -IS 351 0 0 0 0 -IS 352 0 0 0 0 -IS 353 0 0 0 0 -IS 354 0 0 0 0 -IS 355 0 0 0 0 -IS 356 0 0 0 0 -IS 357 0 0 0 0 -IS 358 0 0 0 0 -IS 359 0 0 0 0 -IS 360 0 0 0 0 -IS 361 0 0 0 0 -IS 362 0 0 0 0 -IS 363 0 0 0 0 -IS 364 1 1 0 0 -IS 365 0 0 0 0 -IS 366 0 0 0 0 -IS 367 0 0 0 0 -IS 368 0 0 0 0 -IS 369 0 0 0 0 -IS 370 1 1 0 0 -IS 371 1 1 0 0 -IS 372 0 0 0 0 -IS 373 0 0 0 0 -IS 374 0 0 0 0 -IS 375 0 0 0 0 -IS 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0 0 -IS 439 0 0 0 0 -IS 440 3 3 0 0 -IS 441 1 1 0 0 -IS 442 4 4 0 0 -IS 443 3 3 0 0 -IS 444 1 1 0 0 -IS 445 4 4 0 0 -IS 446 1 1 0 0 -IS 447 1 1 0 0 -IS 448 1 1 0 0 -IS 449 2 2 0 0 -IS 450 3 3 0 0 -IS 451 5 5 0 0 -IS 452 2 2 0 0 -IS 453 3 3 0 0 -IS 454 4 4 0 0 -IS 455 7 7 0 0 -IS 456 3 3 0 0 -IS 457 4 4 0 0 -IS 458 2 2 0 0 -IS 459 3 3 0 0 -IS 460 2 2 0 0 -IS 461 2 2 0 0 -IS 462 2 2 0 0 -IS 463 2 2 0 0 -IS 464 1 1 0 0 -IS 465 6 6 0 0 -IS 466 4 4 0 0 -IS 467 6 6 0 0 -IS 468 1 1 0 0 -IS 469 1 1 0 0 -IS 470 1 1 0 0 -IS 471 3 3 0 0 -IS 472 8 8 0 0 -IS 473 4 4 0 0 -IS 474 2 2 0 0 -IS 475 2 2 0 0 -IS 476 4 4 0 0 -IS 477 6 6 0 0 -IS 478 3 3 0 0 -IS 479 6 6 0 0 -IS 480 7 7 0 0 -IS 481 3 3 0 0 -IS 482 2 2 0 0 -IS 483 1 1 0 0 -IS 484 6 6 0 0 -IS 485 6 6 0 0 -IS 486 6 6 0 0 -IS 487 2 2 0 0 -IS 488 4 4 0 0 -IS 489 3 3 0 0 -IS 490 6 6 0 0 -IS 491 3 3 0 0 -IS 492 5 5 0 0 -IS 493 2 2 0 0 -IS 494 4 4 0 0 -IS 495 0 0 0 0 -IS 496 7 7 0 0 -IS 497 5 5 0 0 -IS 498 4 4 0 0 -IS 499 6 6 0 0 -IS 500 0 0 0 0 -IS 501 2 2 0 0 -IS 502 2 2 0 0 -IS 503 4 4 0 0 -IS 504 3 3 0 0 -IS 505 3 3 0 0 -IS 506 2 2 0 0 -IS 507 4 4 0 0 -IS 508 3 3 0 0 -IS 509 1 1 0 0 -IS 510 7 7 0 0 -IS 511 2 2 0 0 -IS 512 3 3 0 0 -IS 513 7 7 0 0 -IS 514 4 4 0 0 -IS 515 2 2 0 0 -IS 516 2 2 0 0 -IS 517 1 1 0 0 -IS 518 0 0 0 0 -IS 519 2 2 0 0 -IS 520 2 2 0 0 -IS 521 5 5 0 0 -IS 522 6 6 0 0 -IS 523 4 4 0 0 -IS 524 2 2 0 0 -IS 525 1 1 0 0 -IS 526 5 5 0 0 -IS 527 6 6 0 0 -IS 528 0 0 0 0 -IS 529 5 5 0 0 -IS 530 7 7 0 0 -IS 531 4 4 0 0 -IS 532 5 5 0 0 -IS 533 1 1 0 0 -IS 534 5 5 0 0 -IS 535 3 3 0 0 -IS 536 2 2 0 0 -IS 537 3 3 0 0 -IS 538 2 2 0 0 -IS 539 4 4 0 0 -IS 540 2 2 0 0 -IS 541 2 2 0 0 -IS 542 3 3 0 0 -IS 543 4 4 0 0 -IS 544 2 2 0 0 -IS 545 1 1 0 0 -IS 546 2 2 0 0 -IS 547 2 2 0 0 -IS 548 3 3 0 0 -IS 549 5 5 0 0 -IS 550 1 1 0 0 -IS 551 0 0 0 0 -IS 552 0 0 0 0 -IS 553 4 4 0 0 -IS 554 1 1 0 0 -IS 555 5 5 0 0 -IS 556 5 5 0 0 -IS 557 2 2 0 0 -IS 558 2 2 0 0 -IS 559 3 3 0 0 -IS 560 1 1 0 0 -IS 561 1 1 0 0 -IS 562 4 4 0 0 -IS 563 1 1 0 0 -IS 564 1 1 0 0 -IS 565 0 0 0 0 -IS 566 1 1 0 0 -IS 567 1 1 0 0 -IS 568 0 0 0 0 -IS 569 2 2 0 0 -IS 570 1 1 0 0 -IS 571 2 2 0 0 -IS 572 4 4 0 0 -IS 573 0 0 0 0 -IS 574 0 0 0 0 -IS 575 0 0 0 0 -IS 576 1 1 0 0 -IS 577 2 2 0 0 -IS 578 1 1 0 0 -IS 579 2 2 0 0 -IS 580 0 0 0 0 -IS 581 1 1 0 0 -IS 582 0 0 0 0 -IS 583 1 1 0 0 -IS 584 2 2 0 0 -IS 585 0 0 0 0 -IS 586 3 3 0 0 -IS 587 0 0 0 0 -IS 588 0 0 0 0 -IS 589 0 0 0 0 -IS 590 0 0 0 0 -IS 591 0 0 0 0 -IS 592 0 0 0 0 -IS 593 0 0 0 0 -IS 594 2 2 0 0 -IS 595 0 0 0 0 -IS 596 0 0 0 0 -IS 597 1 1 0 0 -IS 598 0 0 0 0 -IS 599 0 0 0 0 -IS 600 1 1 0 0 -IS 601 1 1 0 0 -IS 602 0 0 0 0 -IS 603 0 0 0 0 -IS 604 0 0 0 0 -IS 605 1 1 0 0 -IS 606 0 0 0 0 -IS 607 1 1 0 0 -IS 608 0 0 0 0 -IS 609 0 0 0 0 -IS 610 0 0 0 0 -IS 611 1 1 0 0 +GCC 1 21.50 29.50 33.50 15.50 +GCC 2 30.00 16.00 11.00 43.00 +GCC 3 33.00 25.00 9.00 33.00 +GCC 4 17.00 29.00 13.00 41.00 +GCC 5 37.00 22.00 12.00 29.00 +GCC 6 36.00 26.00 17.00 21.00 +GCC 7 29.50 13.50 31.50 25.50 +GCC 8 50.50 14.50 19.50 15.50 +GCC 9 17.00 33.00 18.00 32.00 +GCC 10 37.00 14.00 21.00 28.00 +GCC 11 20.50 14.50 29.50 35.50 +GCC 12 30.00 24.00 22.00 24.00 +GCC 13 27.00 15.00 21.00 37.00 +GCC 14 24.00 22.00 26.00 28.00 +GCC 15 25.50 20.50 24.50 29.50 +GCC 16 31.00 15.00 20.00 34.00 +GCC 17 28.00 25.00 14.00 33.00 +GCC 18 30.50 28.50 19.50 21.50 +GCC 19 29.00 26.00 21.00 24.00 +GCC 20 22.50 23.50 17.50 36.50 +GCC 21 35.50 17.50 19.50 27.50 +GCC 22 37.50 28.50 15.50 18.50 +GCC 23 31.00 19.00 13.00 37.00 +GCC 24 37.00 12.00 22.00 29.00 +GCC 25 35.50 22.50 17.50 24.50 +GCC 26 33.50 18.50 15.50 32.50 +GCC 27 34.50 14.50 25.50 25.50 +GCC 28 31.00 14.00 24.00 31.00 +GCC 29 30.00 27.00 24.00 19.00 +GCC 30 31.00 20.00 14.00 35.00 +GCC 31 33.50 29.50 13.50 23.50 +GCC 32 42.50 20.50 19.50 17.50 +GCC 33 25.50 23.50 14.50 36.50 +GCC 34 39.50 16.50 20.50 23.50 +GCC 35 32.50 23.50 21.50 22.50 +GCC 36 42.00 25.00 16.00 17.00 +GCC 37 38.00 17.00 19.00 26.00 +GCC 38 24.00 26.00 25.00 25.00 +GCC 39 22.50 41.50 18.50 17.50 +GCC 40 32.00 16.00 21.00 31.00 +GCC 41 33.00 28.00 19.00 20.00 +GCC 42 30.50 25.50 19.50 24.50 +GCC 43 35.00 29.00 15.00 21.00 +GCC 44 20.00 27.00 22.00 31.00 +GCC 45 40.50 21.50 21.50 16.50 +GCC 46 26.50 20.50 22.50 30.50 +GCC 47 38.50 29.50 16.50 15.50 +GCC 48 27.50 24.50 17.50 30.50 +GCC 49 28.50 32.50 10.50 28.50 +GCC 50 46.50 20.50 9.50 23.50 +GCC 51 34.50 28.50 13.50 23.50 +GCC 52 41.50 23.50 20.50 14.50 +GCC 53 20.00 28.00 26.00 26.00 +GCC 54 31.50 18.50 24.50 25.50 +GCC 55 30.50 22.50 16.50 30.50 +GCC 56 33.50 22.50 13.50 30.50 +GCC 57 23.00 24.00 23.00 30.00 +GCC 58 25.00 37.00 19.00 19.00 +GCC 59 34.00 23.00 24.00 19.00 +GCC 60 29.00 28.00 17.00 26.00 +GCC 61 25.50 23.50 24.50 26.50 +GCC 62 31.50 22.50 16.50 29.50 +GCC 63 27.50 28.50 25.50 18.50 +GCC 64 33.50 21.50 25.50 19.50 +GCC 65 35.50 19.50 18.50 26.50 +GCC 66 34.00 25.00 15.00 26.00 +GCC 67 37.00 23.00 19.00 21.00 +GCC 68 36.50 29.50 13.50 20.50 +GCC 69 38.50 19.50 20.50 21.50 +GCC 70 38.50 16.50 18.50 26.50 +GCC 71 25.50 38.50 21.50 14.50 +GCC 72 29.00 29.00 25.00 17.00 +GCC 73 32.50 20.50 21.50 25.50 +GCC 74 28.50 32.50 12.50 26.50 +GCC 75 41.50 12.50 18.50 27.50 +GCC 76 24.50 29.50 23.50 22.50 +GCC 77 36.00 21.00 18.00 25.00 +GCC 78 27.00 34.00 22.00 17.00 +GCC 79 21.50 26.50 25.50 26.50 +GCC 80 34.00 19.00 28.00 19.00 +GCC 81 17.00 26.00 26.00 31.00 +GCC 82 31.00 30.00 23.00 16.00 +GCC 83 31.50 26.50 12.50 29.50 +GCC 84 19.00 41.00 21.00 19.00 +GCC 85 37.50 24.50 16.50 21.50 +GCC 86 15.00 48.00 15.00 22.00 +GCC 87 41.00 16.00 18.00 25.00 +GCC 88 23.50 27.50 27.50 21.50 +GCC 89 26.50 27.50 26.50 19.50 +GCC 90 18.50 23.50 24.50 33.50 +GCC 91 27.00 32.00 22.00 19.00 +GCC 92 23.50 17.50 27.50 31.50 +GCC 93 25.50 37.50 15.50 21.50 +GCC 94 27.00 17.00 24.00 32.00 +GCC 95 26.50 37.50 14.50 21.50 +GCC 96 29.50 25.50 16.50 28.50 +GCC 97 29.00 31.00 21.00 19.00 +GCC 98 18.00 33.00 22.00 27.00 +GCC 99 24.50 33.50 24.50 17.50 +GCC 100 24.50 16.50 24.50 34.50 +GCC 101 25.00 40.00 19.00 16.00 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21.00 28.00 23.00 28.00 +GCC 133 13.50 31.50 35.50 19.50 +GCC 134 24.50 19.50 30.50 25.50 +GCC 135 16.50 23.50 30.50 29.50 +GCC 136 28.00 32.00 15.00 25.00 +GCC 137 22.50 21.50 30.50 25.50 +GCC 138 14.50 34.50 24.50 26.50 +GCC 139 20.50 29.50 24.50 25.50 +GCC 140 17.00 23.00 30.00 30.00 +GCC 141 20.50 23.50 25.50 30.50 +GCC 142 18.00 29.00 38.00 15.00 +GCC 143 22.00 24.00 27.00 27.00 +GCC 144 21.50 30.50 26.50 21.50 +GCC 145 22.00 21.00 29.00 28.00 +GCC 146 25.00 16.00 39.00 20.00 +GCC 147 26.50 22.50 30.50 20.50 +GCC 148 12.50 28.50 36.50 22.50 +GCC 149 26.50 23.50 23.50 26.50 +GCC 150 14.00 29.00 24.00 33.00 +GCC 151 19.50 30.50 32.50 17.50 +GCC 152 18.50 17.50 29.50 34.50 +GCC 153 22.50 22.50 31.50 23.50 +GCC 154 22.00 21.00 29.00 28.00 +GCC 155 21.00 26.00 19.00 34.00 +GCC 156 14.50 23.50 35.50 26.50 +GCC 157 22.00 31.00 23.00 24.00 +GCC 158 22.50 29.50 24.50 23.50 +GCC 159 17.50 12.50 46.50 23.50 +GCC 160 24.50 26.50 26.50 22.50 +GCC 161 13.00 23.00 45.00 19.00 +GCC 162 31.50 16.50 22.50 29.50 +GCC 163 19.50 21.50 35.50 23.50 +GCC 164 29.00 18.00 21.00 32.00 +GCC 165 14.50 17.50 35.50 32.50 +GCC 166 17.50 37.50 28.50 16.50 +GCC 167 16.50 21.50 31.50 30.50 +GCC 168 14.00 25.00 30.00 31.00 +GCC 169 18.50 20.50 23.50 37.50 +GCC 170 19.00 23.00 28.00 30.00 +GCC 171 20.00 28.00 33.00 19.00 +GCC 172 19.00 20.00 32.00 29.00 +GCC 173 24.50 16.50 33.50 25.50 +GCC 174 17.50 23.50 33.50 25.50 +GCC 175 33.50 17.50 35.50 13.50 +GCC 176 16.50 32.50 28.50 22.50 +GCC 177 19.00 22.00 27.00 32.00 +GCC 178 16.00 26.00 30.00 28.00 +GCC 179 18.00 18.00 22.00 42.00 +GCC 180 21.00 22.00 34.00 23.00 +GCC 181 20.50 19.50 35.50 24.50 +GCC 182 32.50 18.50 22.50 26.50 +GCC 183 24.50 13.50 28.50 33.50 +GCC 184 15.00 29.00 30.00 26.00 +GCC 185 15.00 32.00 33.00 20.00 +GCC 186 22.50 23.50 34.50 19.50 +GCC 187 19.00 14.00 40.00 27.00 +GCC 188 27.50 21.50 27.50 23.50 +GCC 189 17.00 22.00 34.00 27.00 +GCC 190 23.00 30.00 23.00 24.00 +GCC 191 25.00 22.00 28.00 25.00 +GCC 192 34.50 24.50 13.50 27.50 +GCC 193 18.50 25.50 25.50 30.50 +GCC 194 18.50 33.50 24.50 23.50 +GCC 195 16.00 26.00 23.00 35.00 +GCC 196 21.50 25.50 24.50 28.50 +GCC 197 20.00 21.00 23.00 36.00 +GCC 198 17.00 21.00 37.00 25.00 +GCC 199 20.50 18.50 25.50 35.50 +GCC 200 21.00 29.00 21.00 29.00 +GCC 201 27.00 21.00 23.00 29.00 +GCC 202 21.50 24.50 19.50 34.50 +GCC 203 21.50 24.50 26.50 27.50 +GCC 204 27.00 29.00 24.00 20.00 +GCC 205 19.50 21.50 22.50 36.50 +GCC 206 26.50 24.50 21.50 27.50 +GCC 207 22.50 21.50 19.50 36.50 +GCC 208 14.00 35.00 29.00 22.00 +GCC 209 16.00 23.00 12.00 49.00 +GCC 210 18.50 19.50 40.50 21.50 +GCC 211 26.00 20.00 22.00 32.00 +GCC 212 21.00 31.00 18.00 30.00 +GCC 213 24.00 15.00 31.00 30.00 +GCC 214 17.50 24.50 25.50 32.50 +GCC 215 26.00 24.00 23.00 27.00 +GCC 216 21.50 17.50 25.50 35.50 +GCC 217 26.00 29.00 17.00 28.00 +GCC 218 20.00 27.00 21.00 32.00 +GCC 219 17.00 21.00 21.00 41.00 +GCC 220 25.50 23.50 23.50 27.50 +GCC 221 21.50 23.50 20.50 34.50 +GCC 222 21.50 21.50 18.50 38.50 +GCC 223 20.00 27.00 28.00 25.00 +GCC 224 22.50 22.50 24.50 30.50 +GCC 225 14.50 35.50 30.50 19.50 +GCC 226 20.00 23.00 26.00 31.00 +GCC 227 20.50 24.50 23.50 31.50 +GCC 228 33.00 19.00 26.00 22.00 +GCC 229 22.50 24.50 18.50 34.50 +GCC 230 21.00 32.00 16.00 31.00 +GCC 231 23.00 28.00 30.00 19.00 +GCC 232 23.50 21.50 12.50 42.50 +GCC 233 21.00 27.00 25.00 27.00 +GCC 234 16.50 27.50 22.50 33.50 +GCC 235 20.00 15.00 28.00 37.00 +GCC 236 28.00 23.00 21.00 28.00 +GCC 237 20.50 19.50 22.50 37.50 +GCC 238 21.50 29.50 24.50 24.50 +GCC 239 20.00 8.00 17.00 55.00 +GCC 240 28.00 24.00 16.00 32.00 +GCC 241 22.50 22.50 16.50 38.50 +GCC 242 29.00 25.00 13.00 33.00 +GCC 243 22.50 15.50 23.50 38.50 +GCC 244 20.50 23.50 16.50 39.50 +GCC 245 28.00 23.00 19.00 30.00 +GCC 246 21.00 29.00 25.00 25.00 +GCC 247 32.00 14.00 13.00 41.00 +GCC 248 18.00 18.00 25.00 39.00 +GCC 249 25.00 23.00 21.00 31.00 +GCC 250 27.50 22.50 17.50 32.50 +GCC 251 13.50 20.50 36.50 29.50 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count -RL 70 1000 +RL 251 200 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions -ID 1 0 1 +ID 1 1 0 +ID 2 1 0 +ID 4 2 0 +ID 10 5 0 +ID 13 1 0 +ID 14 1 0 +ID 15 1 0 +ID 18 1 0 +ID 21 1 0 +ID 22 1 0 +ID 23 2 0 +ID 24 3 0 +ID 29 1 0 +ID 35 2 0 +ID 38 2 0 # Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) -IC 8 0 0 1 0 +IC 2 1 0 0 0 +IC 4 2 0 0 0 +IC 5 3 0 0 0 +IC 210 2 0 0 0 +IC 219 1 0 0 0 +IC 220 1 0 0 0 +IC 224 2 0 0 0 +IC 225 2 0 0 0 +IC 226 1 0 0 0 +IC 228 1 0 0 0 +IC 230 1 0 0 0 +IC 233 1 0 0 0 +IC 234 1 0 0 0 +IC 235 1 0 0 0 +IC 236 1 0 0 0 +IC 239 1 0 0 0 +IC 240 1 0 0 0 +IC 241 1 0 0 0 +IC 247 1 0 0 0 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. -COV [1-1] 1 42 -COV [2-2] 2 59 -COV [3-3] 3 73 -COV [4-4] 4 98 -COV [5-5] 5 128 -COV [6-6] 6 142 -COV [7-7] 7 226 -COV [8-8] 8 241 -COV [9-9] 9 281 -COV [10-10] 10 400 -COV [11-11] 11 450 -COV [12-12] 12 444 -COV [13-13] 13 433 -COV [14-14] 14 423 -COV [15-15] 15 392 -COV [16-16] 16 434 -COV [17-17] 17 294 -COV [18-18] 18 229 -COV [19-19] 19 143 -COV [20-20] 20 143 -COV [21-21] 21 149 -COV [22-22] 22 90 -COV [23-23] 23 41 -COV [24-24] 24 14 +COV [1-1] 1 1 +COV [7-7] 7 1 +COV [18-18] 18 1 +COV [24-24] 24 1 +COV [25-25] 25 249 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile -GCD 0.0 50.000 0.000 0.000 0.000 0.000 0.000 -GCD 44.0 75.000 14.875 14.875 14.875 14.875 14.875 -GCD 46.0 100.000 11.900 11.900 11.900 11.900 11.900 +GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000
--- a/test-data/samtools_stats_out2/cov.tab Mon Oct 20 14:56:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -[1-1] 1 42 -[2-2] 2 59 -[3-3] 3 73 -[4-4] 4 98 -[5-5] 5 128 -[6-6] 6 142 -[7-7] 7 226 -[8-8] 8 241 -[9-9] 9 281 -[10-10] 10 400 -[11-11] 11 450 -[12-12] 12 444 -[13-13] 13 433 -[14-14] 14 423 -[15-15] 15 392 -[16-16] 16 434 -[17-17] 17 294 -[18-18] 18 229 -[19-19] 19 143 -[20-20] 20 143 -[21-21] 21 149 -[22-22] 22 90 -[23-23] 23 41 -[24-24] 24 14
--- a/test-data/samtools_stats_out2/gcc.tab Mon Oct 20 14:56:49 2014 -0400 +++ b/test-data/samtools_stats_out2/gcc.tab Tue Oct 13 12:56:27 2015 -0400 @@ -1,70 +1,252 @@ -1 21.50 23.30 24.50 30.70 -2 21.10 22.20 22.50 34.20 -3 22.20 20.50 26.80 30.50 -4 24.40 21.50 21.50 32.60 -5 23.50 21.10 25.60 29.80 -6 26.30 21.80 20.40 31.50 -7 25.40 20.50 22.00 32.10 -8 23.90 19.20 27.00 29.90 -9 23.70 22.70 22.00 31.60 -10 22.50 22.00 24.10 31.40 -11 22.40 21.50 22.10 34.00 -12 25.20 18.00 24.50 32.30 -13 23.70 20.80 21.70 33.80 -14 24.60 23.00 22.40 30.00 -15 25.50 22.30 22.50 29.70 -16 24.10 21.40 23.60 30.90 -17 24.30 21.00 23.90 30.80 -18 24.40 22.10 22.70 30.80 -19 25.60 20.50 24.70 29.20 -20 25.80 19.60 22.00 32.60 -21 23.20 22.90 23.00 30.90 -22 23.90 22.70 22.60 30.80 -23 25.80 21.30 22.40 30.50 -24 23.50 22.00 22.70 31.80 -25 22.40 21.80 23.10 32.70 -26 22.90 19.90 24.30 32.90 -27 23.10 22.10 24.20 30.60 -28 23.50 22.10 22.90 31.50 -29 24.40 21.80 21.30 32.50 -30 21.90 22.50 22.60 33.00 -31 23.10 20.90 24.20 31.80 -32 24.60 22.10 23.60 29.70 -33 22.80 21.10 22.00 34.10 -34 21.70 22.10 23.60 32.60 -35 24.30 23.20 20.60 31.90 -36 21.60 22.70 24.50 31.20 -37 22.20 23.50 22.20 32.10 -38 24.10 20.80 22.00 33.10 -39 22.20 21.10 26.80 29.90 -40 21.80 24.00 22.90 31.30 -41 25.10 22.90 23.10 28.90 -42 25.50 22.70 22.20 29.60 -43 22.60 23.00 24.10 30.30 -44 21.70 21.60 24.20 32.50 -45 21.80 22.70 21.20 34.30 -46 22.80 22.00 23.80 31.40 -47 23.70 22.30 23.90 30.10 -48 24.30 21.70 24.80 29.20 -49 23.90 22.00 22.90 31.20 -50 23.50 22.40 22.80 31.30 -51 23.30 20.40 24.70 31.60 -52 23.30 20.20 25.10 31.40 -53 23.70 22.00 22.30 32.00 -54 23.30 21.30 25.40 30.00 -55 25.30 21.40 22.60 30.70 -56 24.40 24.10 19.20 32.30 -57 22.00 21.50 24.50 32.00 -58 24.90 21.20 24.20 29.70 -59 24.10 21.70 24.50 29.70 -60 24.80 20.90 25.10 29.20 -61 21.30 21.60 28.10 29.00 -62 23.80 21.80 21.70 32.70 -63 23.30 22.80 23.50 30.40 -64 24.00 21.40 23.50 31.10 -65 24.40 22.80 22.50 30.30 -66 24.70 22.30 21.40 31.60 -67 22.40 21.10 24.60 31.90 -68 24.60 22.90 20.60 31.90 -69 22.40 23.00 23.10 31.50 -70 23.50 19.50 23.90 33.10 +# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent) +1 21.50 29.50 33.50 15.50 +2 30.00 16.00 11.00 43.00 +3 33.00 25.00 9.00 33.00 +4 17.00 29.00 13.00 41.00 +5 37.00 22.00 12.00 29.00 +6 36.00 26.00 17.00 21.00 +7 29.50 13.50 31.50 25.50 +8 50.50 14.50 19.50 15.50 +9 17.00 33.00 18.00 32.00 +10 37.00 14.00 21.00 28.00 +11 20.50 14.50 29.50 35.50 +12 30.00 24.00 22.00 24.00 +13 27.00 15.00 21.00 37.00 +14 24.00 22.00 26.00 28.00 +15 25.50 20.50 24.50 29.50 +16 31.00 15.00 20.00 34.00 +17 28.00 25.00 14.00 33.00 +18 30.50 28.50 19.50 21.50 +19 29.00 26.00 21.00 24.00 +20 22.50 23.50 17.50 36.50 +21 35.50 17.50 19.50 27.50 +22 37.50 28.50 15.50 18.50 +23 31.00 19.00 13.00 37.00 +24 37.00 12.00 22.00 29.00 +25 35.50 22.50 17.50 24.50 +26 33.50 18.50 15.50 32.50 +27 34.50 14.50 25.50 25.50 +28 31.00 14.00 24.00 31.00 +29 30.00 27.00 24.00 19.00 +30 31.00 20.00 14.00 35.00 +31 33.50 29.50 13.50 23.50 +32 42.50 20.50 19.50 17.50 +33 25.50 23.50 14.50 36.50 +34 39.50 16.50 20.50 23.50 +35 32.50 23.50 21.50 22.50 +36 42.00 25.00 16.00 17.00 +37 38.00 17.00 19.00 26.00 +38 24.00 26.00 25.00 25.00 +39 22.50 41.50 18.50 17.50 +40 32.00 16.00 21.00 31.00 +41 33.00 28.00 19.00 20.00 +42 30.50 25.50 19.50 24.50 +43 35.00 29.00 15.00 21.00 +44 20.00 27.00 22.00 31.00 +45 40.50 21.50 21.50 16.50 +46 26.50 20.50 22.50 30.50 +47 38.50 29.50 16.50 15.50 +48 27.50 24.50 17.50 30.50 +49 28.50 32.50 10.50 28.50 +50 46.50 20.50 9.50 23.50 +51 34.50 28.50 13.50 23.50 +52 41.50 23.50 20.50 14.50 +53 20.00 28.00 26.00 26.00 +54 31.50 18.50 24.50 25.50 +55 30.50 22.50 16.50 30.50 +56 33.50 22.50 13.50 30.50 +57 23.00 24.00 23.00 30.00 +58 25.00 37.00 19.00 19.00 +59 34.00 23.00 24.00 19.00 +60 29.00 28.00 17.00 26.00 +61 25.50 23.50 24.50 26.50 +62 31.50 22.50 16.50 29.50 +63 27.50 28.50 25.50 18.50 +64 33.50 21.50 25.50 19.50 +65 35.50 19.50 18.50 26.50 +66 34.00 25.00 15.00 26.00 +67 37.00 23.00 19.00 21.00 +68 36.50 29.50 13.50 20.50 +69 38.50 19.50 20.50 21.50 +70 38.50 16.50 18.50 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38.50 +244 20.50 23.50 16.50 39.50 +245 28.00 23.00 19.00 30.00 +246 21.00 29.00 25.00 25.00 +247 32.00 14.00 13.00 41.00 +248 18.00 18.00 25.00 39.00 +249 25.00 23.00 21.00 31.00 +250 27.50 22.50 17.50 32.50 +251 13.50 20.50 36.50 29.50
--- a/test-data/samtools_stats_out2/gcd.tab Mon Oct 20 14:56:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -0.0 50.000 0.000 0.000 0.000 0.000 0.000 -44.0 75.000 14.875 14.875 14.875 14.875 14.875 -46.0 100.000 11.900 11.900 11.900 11.900 11.900
--- a/test-data/samtools_stats_out2/gcf.tab Mon Oct 20 14:56:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -14.82 0 -31.16 2 -33.42 6 -34.92 4 -36.18 6 -37.44 12 -38.94 28 -40.45 34 -41.96 37 -43.47 46 -44.72 55 -45.98 57 -47.49 68 -48.99 60 -50.50 27 -52.01 18 -53.52 15 -54.77 9 -56.03 4 -57.54 3 -59.05 2 -60.55 4 -62.06 0 -63.32 1
--- a/test-data/samtools_stats_out2/gcl.tab Mon Oct 20 14:56:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -14.07 0 -28.89 1 -30.40 3 -31.91 1 -33.42 2 -34.92 4 -36.18 8 -37.44 16 -38.94 31 -40.45 40 -41.96 39 -43.47 55 -44.72 46 -45.98 61 -47.49 53 -48.99 50 -50.50 32 -52.01 23 -53.52 11 -54.77 9 -56.03 8 -57.54 3 -61.06 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/mpc.tab Tue Oct 13 12:56:27 2015 -0400 @@ -0,0 +1,253 @@ +# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches +1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 0 0 0 0 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--- a/test-data/samtools_stats_out2/sn.tab Mon Oct 20 14:56:49 2014 -0400 +++ b/test-data/samtools_stats_out2/sn.tab Tue Oct 13 12:56:27 2015 -0400 @@ -1,31 +1,33 @@ -raw total sequences: 1000 +# Summary Numbers + +raw total sequences: 200 filtered sequences: 0 -sequences: 1000 +sequences: 200 is sorted: 1 -1st fragments: 500 -last fragments: 500 -reads mapped: 972 -reads mapped and paired: 954 # paired-end technology bit set + both mates mapped -reads unmapped: 28 +1st fragments: 100 +last fragments: 100 +reads mapped: 25 +reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +reads unmapped: 175 reads properly paired: 0 # proper-pair bit set -reads paired: 1000 # paired-end technology bit set +reads paired: 200 # paired-end technology bit set reads duplicated: 0 # PCR or optical duplicate bit set -reads MQ0: 0 # mapped and MQ=0 +reads MQ0: 6 # mapped and MQ=0 reads QC failed: 0 non-primary alignments: 0 -total length: 70000 # ignores clipping -bases mapped: 68040 # ignores clipping -bases mapped (cigar): 68040 # more accurate +total length: 50200 # ignores clipping +bases mapped: 6275 # ignores clipping +bases mapped (cigar): 6275 # more accurate bases trimmed: 0 bases duplicated: 0 -mismatches: 1237 # from NM fields -error rate: 1.818048e-02 # mismatches / bases mapped (cigar) -average length: 70 -maximum length: 70 -average quality: 17.0 -insert size average: 495.1 -insert size standard deviation: 48.9 -inward oriented pairs: 477 +mismatches: 591 # from NM fields +error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +average length: 251 +maximum length: 251 +average quality: 34.7 +insert size average: 0.0 +insert size standard deviation: 0.0 +inward oriented pairs: 0 outward oriented pairs: 0 pairs with other orientation: 0 pairs on different chromosomes: 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_ref.fa Tue Oct 13 12:56:27 2015 -0400 @@ -0,0 +1,239 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG +
--- a/tool_dependencies.xml Mon Oct 20 14:56:49 2014 -0400 +++ b/tool_dependencies.xml Tue Oct 13 12:56:27 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="1.1"> - <repository changeset_revision="c01b111a243b" name="package_samtools_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.2"> + <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>