Mercurial > repos > saketkc > mutation_assessor
changeset 10:ef0e61eded84 draft default tip
Uploaded
| author | saketkc |
|---|---|
| date | Tue, 07 Oct 2014 18:55:39 -0400 |
| parents | 31a4177a694f |
| children | |
| files | mutationassesor_web/mutation_assesor.py mutationassesor_web/mutation_assesor.xml mutationassesor_web/test-data/chasm_input.txt mutationassesor_web/test-data/chasm_output_aminoacids.txt mutationassesor_web/test-data/chasm_output_error.txt mutationassesor_web/test-data/chasm_output_genes.txt mutationassesor_web/test-data/chasm_output_variants.txt mutationassesor_web/test-data/condel_input.txt mutationassesor_web/test-data/condel_input_error.txt mutationassesor_web/test-data/condel_output.csv mutationassesor_web/test-data/ma_empty.csv mutationassesor_web/test-data/ma_nucleotide_output.csv mutationassesor_web/test-data/ma_proper_protein.tsv mutationassesor_web/test-data/ma_protein_output.csv mutationassesor_web/test-data/mutationassessor_input.txt mutationassesor_web/test-data/mutationassessor_output.tsv mutationassesor_web/test-data/polyphen2_full.txt mutationassesor_web/test-data/polyphen2_input.txt mutationassesor_web/test-data/polyphen2_log.txt mutationassesor_web/test-data/polyphen2_short.txt mutationassesor_web/test-data/polyphen2_snp.txt mutationassesor_web/test-data/transfic_output.csv |
| diffstat | 21 files changed, 49 insertions(+), 248 deletions(-) [+] |
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--- a/mutationassesor_web/mutation_assesor.py Tue Apr 15 12:21:30 2014 -0400 +++ b/mutationassesor_web/mutation_assesor.py Tue Oct 07 18:55:39 2014 -0400 @@ -4,7 +4,8 @@ import os import argparse import re - +import csv +import StringIO __url__ = 'http://mutationassessor.org/' @@ -37,8 +38,9 @@ Server returned %s . Output: %s """ % (request.status_code, response)) - with open(args.output, 'wb') as fp: - fp.write(response) + r = StringIO.StringIO(response) + reader = csv.reader(r, delimiter=",") + csv.writer(open(args.output, "wb"), delimiter='\t').writerows(reader) if __name__ == '__main__': parser = argparse.ArgumentParser(description="Process input output paths")
--- a/mutationassesor_web/mutation_assesor.xml Tue Apr 15 12:21:30 2014 -0400 +++ b/mutationassesor_web/mutation_assesor.xml Tue Oct 07 18:55:39 2014 -0400 @@ -37,10 +37,15 @@ <output name="output" file="ma_nucleotide_output.csv"/> </test> <test> - <param name="input" value="ma_proper_protein.tsv"/> + <param name="input" value="ma_proper_protein.csv"/> <param name="protein" value="yes"/> <output name="output" file="ma_protein_output.csv"/> </test> + <test> + <param name="input" value="mutationassessor_input.txt"/> + <param name="protein" value="yes"/> + <output name="output" file="mutationassessor_output.tsv" lines_diff="2"/> + </test> </tests> <help>
--- a/mutationassesor_web/test-data/chasm_input.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -TR1 chr22 30421786 + A T -TR2 chr22 29446079 + A G -TR3 chr22 29446079 + A G -TR4 chr22 40814500 - A G -TR5 chr22 40815256 + C T
--- a/mutationassesor_web/test-data/chasm_output_aminoacids.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#Amino Acid Level Analysis Report -#2014-04-14 18:52:00.963260 -#Analysis done at http://www.cravat.us. -#Input file: dataset_34.dat -#This report shows analysis results at amino acid level. -#Input coordinate was hg19 genomic. -#For more information on CRAVAT, visit http://www.cravat.us. -# -Transcript Amino acid position Sequence Ontology Reference amino acid(s) Alternate amino acid(s) HUGO symbol Other transcripts Occurrences in study [amino acid change] Transcript by COSMIC AA change by COSMIC Occurrences in COSMIC [amino acid change] Occurrences in COSMIC by primary sites [amino acid change] -NM_021090.3 1198 MS N I MTMR3 NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I 1 0 -NM_001206998.1 637 MS H R ZNRF3 NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 2 0 -NM_020831.3 648 MS S G MKL1 ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G 1 ENST00000355630 p.S648G (stomach 1) 1 stomach(1 ) -NM_020831.3 396 MS A T MKL1 ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T 1 0
--- a/mutationassesor_web/test-data/chasm_output_error.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -# End of input format error output. If nothing is above this line, there was no format error in the input. \ No newline at end of file
--- a/mutationassesor_web/test-data/chasm_output_genes.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#Gene Level Analysis Report -#2014-04-14 18:52:00.963904 -#Analysis done at http://www.cravat.us. -#Input file: dataset_34.dat -#This report shows analysis results at gene level. -#The composite p-value (Stouffer's combined p-value) and composite FDR of a gene show how probable it is to get the same p-value distribution for the gene as that obtained from the input variants by chance. -#Input coordinate was hg19 genomic. -#Tissue type for CHASM analysis: Other -#For more information on CRAVAT, visit http://www.cravat.us. -# -HUGO symbol Best driver score from representative transcripts Composite p value Composite FDR Occurrences in study [gene mutated] Occurrences in COSMIC [gene mutated] Occurrences in COSMIC by primary sites [gene mutated] -MTMR3 0.6 0.3364 0.55 1 102 upper_aerodigestive_tract(2);large_intestine(24);haematopoietic_and_lymphoid_tissue(5);endometrium(12);urinary_tract(4);oesophagus(1);liver(3);skin(17);lung(17);ovary(5);prostate(2);kidney(4);breast(6 ) -ZNRF3 0.514 0.171 0.55 2 73 upper_aerodigestive_tract(2);large_intestine(19);autonomic_ganglia(1);haematopoietic_and_lymphoid_tissue(2);endometrium(12);urinary_tract(2);lung(16);liver(5);skin(1);oesophagus(3);ovary(2);NS(1);prostate(2);kidney(3);breast(2 ) -MKL1 0.728 0.793956248886469 1 2 68 large_intestine(15);stomach(2);central_nervous_system(1);haematopoietic_and_lymphoid_tissue(3);endometrium(13);urinary_tract(1);lung(19);breast(3);skin(1);ovary(5);kidney(4);liver(1 )
--- a/mutationassesor_web/test-data/chasm_output_variants.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#Variant Level Analysis Report -#2014-04-14 18:52:00.964521 -#Analysis done at http://www.cravat.us. -#Input file: dataset_34.dat -#This report shows analysis results at variant level. -#Input coordinate was hg19 genomic. -#Tissue type for CHASM analysis: Other -#For more information on CRAVAT, visit http://www.cravat.us. -# -ID Chromosome Position Strand Reference base Alternate base Sample ID HUGO symbol Transcript Transcript strand Codon change Amino acid position Sequence Ontology Reference amino acid(s) Alternate amino acid(s) Other transcripts Mappability Warning Driver score of representative transcript (driver mutations close to 0) Empirical p-value FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations) Best driver score and transcript All transcripts and driver scores dbSNP 1000 Genomes allele frequency ESP6500 allele frequency (European American) ESP6500 allele frequency (African American) Occurrences in study [exact nucleotide change] Transcript by COSMIC AA change by COSMIC Occurrences in COSMIC [exact nucleotide change] Occurrences in COSMIC by primary sites [exact nucleotide change] -TR1 CHR22 30421786 + A T No_sample_ID MTMR3 NM_021090.3 + aAc>aTc 1198 MS N I NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I 0.6(NM_021090.3:N1198I) 0.3364 0.60 0.572(ENST00000323630:N1062I) ENST00000323630:N1062I(0.572),ENST00000406629:N1170I(0.602),ENST00000401950:N1198I(0.6),ENST00000351488:N1161I(0.572),NM_153050.2:N1170I(0.572),ENST00000333027:N1170I(0.572),NM_021090.3:N1198I(0.6),NM_153051.2:N1161I(0.572) rs75623810 0.00778388278388 0 0.0226963 1 -TR2 CHR22 29446079 + A G No_sample_ID ZNRF3 NM_001206998.1 + cAc>cGc 637 MS H R NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 0.514(NM_001206998.1:H637R) 0.1710 0.60 0.442(ENST00000544604:H637R) ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514) rs62641746 0 0.00569767 0.000907853 2 -TR3 CHR22 29446079 + A G No_sample_ID ZNRF3 NM_001206998.1 + cAc>cGc 637 MS H R NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 0.514(NM_001206998.1:H637R) 0.1710 0.60 0.442(ENST00000544604:H637R) ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514) rs62641746 0 0.00569767 0.000907853 2 -TR4 CHR22 40814500 - A G No_sample_ID MKL1 NM_020831.3 - Agc>Ggc 648 MS S G ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G 0.728(NM_020831.3:S648G) 0.6890 0.80 0.708(ENST00000402042:S598G) ENST00000407029:S648G(0.728),NM_020831.3:S648G(0.728),ENST00000396617:S648G(0.728),ENST00000355630:S648G(0.728),ENST00000402042:S598G(0.708) rs878756 0.419871794872 0.396977 0.860645 1 ENST00000355630 p.S648G (stomach 1) 1 stomach(1) -TR5 CHR22 40815256 + C T No_sample_ID MKL1 NM_020831.3 - Gcc>Acc 396 MS A T ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T 0.748(NM_020831.3:A396T) 0.7476 0.80 0.748(ENST00000407029:A396T) ENST00000407029:A396T(0.748),NM_020831.3:A396T(0.748),ENST00000396617:A396T(0.748),ENST00000355630:A396T(0.748),ENST00000402042:A346T(0.754) rs34736200 0.0201465201465 0.00127907 0.0832955 1
--- a/mutationassesor_web/test-data/condel_input.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -9 32473058 32473058 A -7 43918688 43918688 C -7 38471790 38471790 A -6 88372821 88372821 A -5 41934236 41934236 G
--- a/mutationassesor_web/test-data/condel_input_error.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -22 30421786 T -22 29446079 G -22 40814500 G -22 40815256 T -
--- a/mutationassesor_web/test-data/condel_output.csv Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -#id location allele gene hgnc hgncdesc transcript ensp sw protein_position amino_acids uploaded_variation cdna_position cds_position codons existing_variation sift polyphen mass condel condelLabel -19 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000428293 ENSP00000390734 NA 386 T/M 7_38471790_A 1226 1157 aCg/aTg COSM53413 0.01 0.998 NA 0.880 deleterious -17 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000447717 ENSP00000402803 NA 82 L/R 7_43918688_C 762 245 cTc/cGc COSM53414 0.05 0.995 NA 0.803 deleterious -18 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000546266 ENSP00000444695 NA 455 A/T 6_88372821_A 1720 1363 Gcc/Acc COSM53412 0.01 0.93 NA 0.782 deleterious -15 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000392844 ENSP00000376586 ORC3_HUMAN 598 A/T 6_88372821_A 1840 1792 Gcc/Acc COSM53412 0.01 0.93 1.95 0.782 deleterious -16 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000452292 ENSP00000411130 NA 536 A/T 6_88372821_A 1615 1606 Gcc/Acc COSM53412 0.01 0.266 NA 0.032 neutral -13 5:41934236 G ENSG00000151876 FBXO4 F-box protein 4 ENST00000509134 ENSP00000421749 NA 242 K/E 5_41934236_G 733 724 Aag/Gag COSM53411 0.68 0.01 NA 0.001 neutral -14 5:41934236 G ENSG00000151876 FBXO4 F-box protein 4 ENST00000281623 ENSP00000281623 FBX4_HUMAN 242 K/E 5_41934236_G 780 724 Aag/Gag COSM53411 0.76 0.001 0 0.000 neutral -11 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000379882 ENSP00000369212 NA 598 L/F 9_32473058_A 1952 1794 ttA/ttT COSM53415 0.01 0.96 NA 0.808 deleterious -12 5:41934236 G ENSG00000151876 FBXO4 F-box protein 4 ENST00000296812 ENSP00000296812 NA 242 K/E 5_41934236_G 780 724 Aag/Gag COSM53411 0.67 0.01 NA 0.001 neutral -21 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000353242 ENSP00000342268 NA 156 T/M 7_38471790_A 1226 467 aCg/aTg COSM53413 0 0.983 NA 0.929 deleterious -20 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000356264 ENSP00000348602 AMPH_HUMAN 386 T/M 7_38471790_A 1373 1157 aCg/aTg COSM53413 0.01 0.998 1.79 0.880 deleterious -22 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000257789 ENSP00000257789 NA 599 A/T 6_88372821_A 1829 1795 Gcc/Acc COSM53412 0.01 0.983 NA 0.835 deleterious -23 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000325590 ENSP00000317441 NA 386 T/M 7_38471790_A 1226 1157 aCg/aTg COSM53413 0.02 0.998 NA 0.857 deleterious -24 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000441628 ENSP00000415085 NA 137 T/M 7_38471790_A 408 410 aCg/aTg COSM53413 0 0.983 NA 0.929 deleterious -3 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000223341 ENSP00000223341 NA 82 L/R 7_43918688_C 622 245 cTc/cGc COSM53414 0.05 0.995 NA 0.803 deleterious -2 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000545044 ENSP00000443055 NA 440 L/F 9_32473058_A 1810 1320 ttA/ttT COSM53415 0 0.918 NA 0.869 deleterious -10 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000379883 ENSP00000369213 DDX58_HUMAN 643 L/F 9_32473058_A 2087 1929 ttA/ttT COSM53415 0.01 0.96 3.78 0.808 deleterious -1 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000402306 ENSP00000384955 NA 116 L/R 7_43918688_C 387 347 cTc/cGc COSM53414 0.05 0.995 NA 0.803 deleterious -0 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000542096 ENSP00000442160 NA 572 L/F 9_32473058_A 2292 1716 ttA/ttT COSM53415 0.01 0.96 NA 0.808 deleterious -7 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000453200 ENSP00000396918 URGCP_HUMAN 125 L/R 7_43918688_C 868 374 cTc/cGc COSM53414 0.05 0.995 2.545 0.803 deleterious -6 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000443736 ENSP00000392136 NA 82 L/R 7_43918688_C 420 245 cTc/cGc COSM53414 0.05 0.995 NA 0.803 deleterious -5 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000455877 ENSP00000392963 NA 82 L/R 7_43918688_C 469 245 cTc/cGc COSM53414 0 0.995 NA 0.958 deleterious -4 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000426198 ENSP00000389990 NA 82 L/R 7_43918688_C 640 245 cTc/cGc COSM53414 0.09 0.995 NA 0.467 neutral -9 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000379868 ENSP00000369197 NA 440 L/F 9_32473058_A 1823 1320 ttA/ttT COSM53415 0.01 0.96 NA 0.808 deleterious -8 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000336086 ENSP00000336872 NA 82 L/R 7_43918688_C 2482 245 cTc/cGc COSM53414 0.05 0.995 NA 0.803 deleterious
--- a/mutationassesor_web/test-data/ma_nucleotide_output.csv Tue Apr 15 12:21:30 2014 -0400 +++ b/mutationassesor_web/test-data/ma_nucleotide_output.csv Tue Oct 07 18:55:39 2014 -0400 @@ -1,4 +1,4 @@ -"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site" -"1","hg19,13,32912555,G,T","D1355Y","BRCA2","http://getma.org/?cm=msa&ty=f&p=BRCA2_HUMAN&rb=1247&re=1420&var=D1355Y","","low","1.24","BRCA2_HUMAN","NP_000050","14","chr13:32912555","","","","" -"2","hg19,7,55178574,G,A","","","","","","","","","0","","","","","" -"3","hg19,7,55178574,G,A","","","","","","","","","0","","","","","" + Mutation AA variant Gene MSA PDB Func. Impact FI score Uniprot Refseq MSA height Codon start position Func. region Protein bind.site DNA/RNA bind.site small.mol bind.site +1 hg19,13,32912555,G,T D1355Y BRCA2 http://getma.org/?cm=msa&ty=f&p=BRCA2_HUMAN&rb=1247&re=1420&var=D1355Y low 1.24 BRCA2_HUMAN NP_000050 14 chr13:32912555 +2 hg19,7,55178574,G,A 0 +3 hg19,7,55178574,G,A 0
--- a/mutationassesor_web/test-data/ma_proper_protein.tsv Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -EGFR_HUMAN R521K -EGFR_HUMAN R98Q Polymorphism -EGFR_HUMAN G719D disease -NP_000537 G356A -NP_000537 G360A dbSNP:rs35993958 -NP_000537 S46A Abolishes phosphorylation
--- a/mutationassesor_web/test-data/ma_protein_output.csv Tue Apr 15 12:21:30 2014 -0400 +++ b/mutationassesor_web/test-data/ma_protein_output.csv Tue Oct 07 18:55:39 2014 -0400 @@ -1,7 +1,7 @@ -"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site" -"1","EGFR_HUMAN R521K","R521K","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=482&re=681&var=R521K","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=482&to=681&var=R521K","neutral","0.405","EGFR_HUMAN","NP_005219","399","chr7:55196748","1","1","","" -"2","EGFR_HUMAN R98Q","R98Q","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=57&re=168&var=R98Q","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=57&to=168&var=R98Q","neutral","0.6","EGFR_HUMAN","NP_005219","181","chr7:55178543","","","","" -"3","EGFR_HUMAN G719D","G719D","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719D","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719D","medium","3.115","EGFR_HUMAN","NP_005219","700","chr7:55209201","1","1","","0UN IRE FMM ANP CY7 HYZ 03P ITI DKI 685 T95 T74 ZZY M97 6XP 0K0 KRW 0JJ 0K1 P17 112 1N1 JIN STI P5C 585 S19 P16 VX6 P3Y SX7 ACK B90 AMP ZD6 STU 7PY BI9 BII ATP ADP 4ST VG8 YAM P1E 7X4 7X5 7X6 7X8 349 3JZ" -"4","NP_000537 G356A","G356A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=318&re=359&var=G356A","http://getma.org/pdb.php?prot=P53_HUMAN&from=318&to=359&var=G356A","neutral","-0.895","P53_HUMAN","NP_000537","45","chr17:7514684","","1","","" -"5","NP_000537 G360A","G360A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=360&re=393&var=G360A","","medium","2.25","P53_HUMAN","NP_000537","15","chr17:7514672","","","","" -"6","NP_000537 S46A","S46A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=30&re=94&var=S46A","http://getma.org/pdb.php?prot=P53_HUMAN&from=30&to=94&var=S46A","neutral","0.55","P53_HUMAN","NP_000537","5","chr17:7520274","1","1","","" + Mutation AA variant Gene MSA PDB Func. Impact FI score Uniprot Refseq MSA height Codon start position Func. region Protein bind.site DNA/RNA bind.site small.mol bind.site +1 EGFR_HUMAN,R521K EGFR_HUMAN,R521K 0 +2 EGFR_HUMAN,R98Q,POLYMORPHISM EGFR_HUMAN,R98Q,POLYMORPHISM 0 +3 EGFR_HUMAN,G719D,DISEASE EGFR_HUMAN,G719D,DISEASE 0 +4 NP_000537,G356A NP_000537,G356A 0 +5 NP_000537,G360A,DBSNP:RS35993958 NP_000537,G360A,DBSNP:RS35993958 0 +6 NP_000537,S46A,ABOLISHES,PHOSPHORYLATION NP_000537,S46A,ABOLISHES,PHOSPHORYLATION 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/mutationassessor_input.txt Tue Oct 07 18:55:39 2014 -0400 @@ -0,0 +1,13 @@ +EGFR_HUMAN G719S +EGFR_HUMAN G724S +EGFR_HUMAN E734K +EGFR_HUMAN L747F +EGFR_HUMAN R748P +EGFR_HUMAN Q787R +EGFR_HUMAN T790M +EGFR_HUMAN L833V +EGFR_HUMAN V834L +EGFR_HUMAN L858R +EGFR_HUMAN L861Q +EGFR_HUMAN G873E +EGFR_HUMAN R962G
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutationassesor_web/test-data/mutationassessor_output.tsv Tue Oct 07 18:55:39 2014 -0400 @@ -0,0 +1,14 @@ + Mutation AA variant Gene MSA PDB Func. Impact FI score Uniprot Refseq MSA height Codon start position Func. region Protein bind.site DNA/RNA bind.site small.mol bind.site +1 EGFR_HUMAN G719S G719S EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719S http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719S high 3.88 EGFR_HUMAN NP_005219 700 chr7:55209201 1 1 0UN IRE FMM ANP CY7 HYZ 03P ITI DKI 685 T95 T74 ZZY M97 6XP 0K0 KRW 0JJ 0K1 P17 112 1N1 JIN STI P5C 585 S19 P16 VX6 P3Y SX7 ACK B90 AMP ZD6 STU 7PY BI9 BII ATP ADP 4ST VG8 YAM P1E 7X4 7X5 7X6 7X8 349 3JZ +2 EGFR_HUMAN G724S G724S EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G724S http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G724S medium 2.7 EGFR_HUMAN NP_005219 700 chr7:55209216 1 ANP 112 ATP AMP 057 +3 EGFR_HUMAN E734K E734K EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=E734K http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=E734K neutral -0.08 EGFR_HUMAN NP_005219 700 chr7:55209924 +4 EGFR_HUMAN L747F L747F EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L747F http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L747F low 1.9 EGFR_HUMAN NP_005219 700 chr7:55209963 1 +5 EGFR_HUMAN R748P R748P EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=R748P http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=R748P low 1.155 EGFR_HUMAN NP_005219 700 chr7:55209966 1 VX6 STU S19 +6 EGFR_HUMAN Q787R Q787R EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=Q787R http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=Q787R neutral 0.225 EGFR_HUMAN NP_005219 700 chr7:55216555 +7 EGFR_HUMAN T790M T790M EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=T790M http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=T790M low 1.17 EGFR_HUMAN NP_005219 700 chr7:55216564 1 1 AQ4 AEE CY0 DJK IRE FMM ANP CY7 HYZ ITI POX 03P 03Q GW7 DKI 477 685 0JE T95 T74 ZZY PFY M97 6XP 0K0 VGH KRW 0JJ 0K1 PRC STI P17 112 1N1 7MP GIN JIN B91 919 9DP DB8 4ST 627 0JK P5C S19 P16 406 VX6 P3Y NIL SX7 0LI XY3 ACK PP1 X2M B90 AMP ZD6 X2K X2L ACP DBQ STU 057 7PY BII ATP ADP YAM P1E 7X4 7X5 7X6 7X8 349 3JZ 4JZ +8 EGFR_HUMAN L833V L833V EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L833V http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L833V neutral -1.13 EGFR_HUMAN NP_005219 700 chr7:55226933 1 STI GIN B91 919 406 NIL 0LI +9 EGFR_HUMAN V834L V834L EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=V834L http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=V834L low 1.87 EGFR_HUMAN NP_005219 700 chr7:55226936 1 STI GIN 406 0LI XY3 PTR +10 EGFR_HUMAN L858R L858R EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L858R http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L858R medium 3.32 EGFR_HUMAN NP_005219 700 chr7:55227008 1 FMM CY7 HYZ ITI POX 03P GW7 BI9 ATP VG8 YAM +11 EGFR_HUMAN L861Q L861Q EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=L861Q http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=L861Q neutral 0.735 EGFR_HUMAN NP_005219 700 chr7:55227017 1 GIN PTR +12 EGFR_HUMAN G873E G873E EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G873E http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G873E neutral 0.775 EGFR_HUMAN NP_005219 700 chr7:55227053 1 +13 EGFR_HUMAN R962G R962G EGFR http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=R962G http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=R962G low 0.805 EGFR_HUMAN NP_005219 700 chr7:55235538 1
--- a/mutationassesor_web/test-data/polyphen2_full.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#o_acc o_pos o_aa1 o_aa2 rsid acc pos aa1 aa2 nt1 nt2 prediction based_on effect pph2_class pph2_prob pph2_FPR pph2_TPR pph2_FDR site region PHAT dScore Score1 Score2 MSAv Nobs Nstruct Nfilt PDB_id PDB_pos PDB_ch ident length NormASA SecStr MapReg dVol dProp B-fact H-bonds AveNHet MinDHet AveNInt MinDInt AveNSit MinDSit Transv CodPos CpG MinDJxn PfamHit IdPmax IdPSNP IdQmin -Q13615-2 1170 N I ? Q13615-2 1170 N I A T probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 ? ? ? +2.214 -1.705 -3.919 2 37 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0 -2313 ? 1.268 ? 47.09 # chr22:30421786|AT|uc003agu.3+|MTMR3|NP_694690 -Q13615 1198 N I ? Q13615 1198 N I A T probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 NO NO ? +2.296 -1.580 -3.876 2 38 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0 -3099 NO 1.010 ? 45.58 # chr22:30421786|AT|uc003agv.3+|MTMR3|NP_066576 -Q13615-3 1161 N I ? Q13615-3 1161 N I A T probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 ? ? ? +2.214 -1.705 -3.919 2 37 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0 -3099 ? 1.275 ? 47.37 # chr22:30421786|AT|uc003agw.3+|MTMR3|NP_694691 -Q9ULT6 637 H R ? Q9ULT6 637 H R A G benign alignment ? neutral 0.002 0.704 0.987 0.452 NO NO ? +0.398 -2.258 -2.656 2 47 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 2 +858 NO 20.363 20.363 77.46 # chr22:29446079|AG|uc003aeg.2+|ZNRF3|NP_115549 -Q9ULT6 637 H R ? Q9ULT6 637 H R A G benign alignment ? neutral 0.002 0.704 0.987 0.452 NO NO ? +0.398 -2.258 -2.656 2 47 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 2 -1599 NO 20.363 20.363 77.46 # chr22:29446079|AG|uc003aeh.1+|ZNRF3|NP_115549 -Q969V6 648 S C ? Q969V6 648 S C A T possibly damaging alignment ? deleterious 0.89 0.0639 0.821 0.0953 NO COMPBIAS ? +2.837 -1.909 -4.746 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.320 ? 90.33 # chr22:40814500|TA|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R A C benign alignment ? neutral 0.167 0.131 0.92 0.162 NO COMPBIAS ? +1.814 -1.909 -3.723 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 2.525 ? 90.33 # chr22:40814500|TG|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S C ? Q969V6 648 S C A T possibly damaging alignment ? deleterious 0.89 0.0639 0.821 0.0953 NO COMPBIAS ? +2.837 -1.909 -4.746 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.320 ? 90.33 # chr22:40814500|TA|uc003ayw.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R A C benign alignment ? neutral 0.167 0.131 0.92 0.162 NO COMPBIAS ? +1.814 -1.909 -3.723 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 2.525 ? 90.33 # chr22:40814500|TG|uc003ayw.1-|MKL1|NP_065882 -E7ER32 648 S C ? E7ER32 648 S C A T possibly damaging alignment ? deleterious 0.953 0.0514 0.788 0.0812 NO NO ? +2.837 -1.909 -4.746 2 33 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.255 ? 87.22 # chr22:40814500|TA|uc010gye.1-|MKL1| -E7ER32 648 S R ? E7ER32 648 S R A C benign alignment ? neutral 0.337 0.111 0.901 0.142 NO NO ? +1.814 -1.909 -3.723 2 33 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 2.402 ? 87.22 # chr22:40814500|TG|uc010gye.1-|MKL1| -B0QY83 598 S C ? B0QY83 598 S C A T possibly damaging alignment_mz ? deleterious 0.726 0.0797 0.856 0.112 NO NO ? +2.847 -1.931 -4.778 3 31 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.615 ? 91.49 # chr22:40814500|TA|uc010gyf.1-|MKL1|NP_065882 -B0QY83 598 S R ? B0QY83 598 S R A C benign alignment_mz ? neutral 0.047 0.168 0.942 0.195 NO NO ? +1.674 -1.931 -3.605 3 31 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 5.560 ? 91.49 # chr22:40814500|TG|uc010gyf.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T G A benign alignment ? neutral 0.009 0.233 0.961 0.247 NO NO ? +0.097 -1.540 -1.637 2 39 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 21.659 21.659 88.08 # chr22:40815256|CT|uc003ayv.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T G A benign alignment ? neutral 0.009 0.233 0.961 0.247 NO NO ? +0.097 -1.540 -1.637 2 39 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 21.659 21.659 88.08 # chr22:40815256|CT|uc003ayw.1-|MKL1|NP_065882 -E7ER32 396 A T ? E7ER32 396 A T G A benign alignment ? neutral 0.009 0.233 0.961 0.247 NO NO ? +0.097 -1.540 -1.637 2 39 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 20.554 20.554 83.58 # chr22:40815256|CT|uc010gye.1-|MKL1| -B0QY83 346 A T ? B0QY83 346 A T G A benign alignment_mz ? neutral 0.008 0.239 0.963 0.252 NO NO ? +0.456 -1.547 -2.003 3 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 21.940 21.940 89.22 # chr22:40815256|CT|uc010gyf.1-|MKL1|NP_065882 -## Sources: -## Predictions: PolyPhen-2 v2.2.2r398 -## Sequences: UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011) -## Structures: PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures) -## Genes: UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
--- a/mutationassesor_web/test-data/polyphen2_input.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -chr22:30421786 A/T -chr22:29446079 A/G -chr22:40814500 A/G -chr22:40815256 C/T -
--- a/mutationassesor_web/test-data/polyphen2_log.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -=========================== -Stage 1/7: Validating input -=========================== -No errors - -=============================== -Stage 2/7: Mapping genomic SNPs -=============================== -WARNING: (chr22:40814500 - uc003ayv.1) None of the input alleles (A/G) matches reference allele (T) -WARNING: (chr22:40814500 - uc003ayw.1) None of the input alleles (A/G) matches reference allele (T) -WARNING: (chr22:40814500 - uc010gye.1) None of the input alleles (A/G) matches reference allele (T) -WARNING: (chr22:40814500 - uc010gyf.1) None of the input alleles (A/G) matches reference allele (T) -Total errors/warnings: 4 - -============================ -Stage 3/7: Collecting output -============================ -No errors - -=============================================== -Stage 4/7: Building MSA and annotating proteins -=============================================== -No errors - -============================ -Stage 5/7: Collecting output -============================ -No errors - -===================== -Stage 6/7: Predicting -===================== -No errors - -============================= -Stage 7/7: Generating reports -============================= -No errors
--- a/mutationassesor_web/test-data/polyphen2_short.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#o_acc o_pos o_aa1 o_aa2 rsid acc pos aa1 aa2 prediction pph2_prob pph2_FPR pph2_TPR -Q13615-2 1170 N I ? Q13615-2 1170 N I probably damaging 0.998 0.0112 0.273 # chr22:30421786|AT|uc003agu.3+|MTMR3|NP_694690 -Q13615 1198 N I ? Q13615 1198 N I probably damaging 0.998 0.0112 0.273 # chr22:30421786|AT|uc003agv.3+|MTMR3|NP_066576 -Q13615-3 1161 N I ? Q13615-3 1161 N I probably damaging 0.998 0.0112 0.273 # chr22:30421786|AT|uc003agw.3+|MTMR3|NP_694691 -Q9ULT6 637 H R ? Q9ULT6 637 H R benign 0.002 0.704 0.987 # chr22:29446079|AG|uc003aeg.2+|ZNRF3|NP_115549 -Q9ULT6 637 H R ? Q9ULT6 637 H R benign 0.002 0.704 0.987 # chr22:29446079|AG|uc003aeh.1+|ZNRF3|NP_115549 -Q969V6 648 S C ? Q969V6 648 S C possibly damaging 0.89 0.0639 0.821 # chr22:40814500|TA|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R benign 0.167 0.131 0.92 # chr22:40814500|TG|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S C ? Q969V6 648 S C possibly damaging 0.89 0.0639 0.821 # chr22:40814500|TA|uc003ayw.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R benign 0.167 0.131 0.92 # chr22:40814500|TG|uc003ayw.1-|MKL1|NP_065882 -E7ER32 648 S C ? E7ER32 648 S C possibly damaging 0.953 0.0514 0.788 # chr22:40814500|TA|uc010gye.1-|MKL1| -E7ER32 648 S R ? E7ER32 648 S R benign 0.337 0.111 0.901 # chr22:40814500|TG|uc010gye.1-|MKL1| -B0QY83 598 S C ? B0QY83 598 S C possibly damaging 0.726 0.0797 0.856 # chr22:40814500|TA|uc010gyf.1-|MKL1|NP_065882 -B0QY83 598 S R ? B0QY83 598 S R benign 0.047 0.168 0.942 # chr22:40814500|TG|uc010gyf.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T benign 0.009 0.233 0.961 # chr22:40815256|CT|uc003ayv.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T benign 0.009 0.233 0.961 # chr22:40815256|CT|uc003ayw.1-|MKL1|NP_065882 -E7ER32 396 A T ? E7ER32 396 A T benign 0.009 0.233 0.961 # chr22:40815256|CT|uc010gye.1-|MKL1| -B0QY83 346 A T ? B0QY83 346 A T benign 0.008 0.239 0.963 # chr22:40815256|CT|uc010gyf.1-|MKL1|NP_065882 -## Sources: -## Predictions: PolyPhen-2 v2.2.2r398 -## Sequences: UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011) -## Structures: PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures) -## Genes: UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
--- a/mutationassesor_web/test-data/polyphen2_snp.txt Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -#snp_pos str gene transcript ccid ccds cciden refa type ntpos nt1 nt2 flanks trv cpg jxdon jxacc exon cexon jxc dgn cdnpos frame cdn1 cdn2 aa1 aa2 aapos spmap spacc spname refs_acc dbrsid dbobsrvd dbavHet dbavHetSE dbRmPaPt comments -chr22:30421786 + MTMR3 uc003agu.3 ? CCDS13871.1 1 A/T missense 142629 A T AC 1 0 -2313 -168 20/20 18/18 ? 0 1170 1 AAC ATC N I 1170 1 Q13615-2 MTMR3_HUMAN NP_694690 rs75623810 A/T 0.016564 0.089485 A>A>A -chr22:30421786 + MTMR3 uc003agv.3 16552 CCDS13870.1 1 A/T missense 142629 A T AC 1 0 -3099 -168 20/20 18/18 ? 0 1198 1 AAC ATC N I 1198 1 Q13615 MTMR3_HUMAN NP_066576 rs75623810 A/T 0.016564 0.089485 A>A>A -chr22:30421786 + MTMR3 uc003agw.3 ? CCDS46682.1 1 A/T missense 142629 A T AC 1 0 -3099 -168 19/19 17/17 ? 0 1161 1 AAC ATC N I 1161 1 Q13615-3 MTMR3_HUMAN NP_694691 rs75623810 A/T 0.016564 0.089485 A>A>A -chr22:29446079 + ZNRF3 uc003aeg.2 16531 CCDS42999.1 1 A/G missense 166190 A G CC 0 2 +858 -895 8/9 7/8 ? 0 537 1 CAC CGC H R 637 1 Q9ULT6 ZNRF3_HUMAN NP_115549 rs62641746 A/G 0.030762 0.120144 A>A>A -chr22:29446079 + ZNRF3 uc003aeh.1 ? CCDS42999.1 0.982 A/G missense 63040 A G CC 0 2 -1599 -895 7/7 7/7 ? 0 537 1 CAC CGC H R 637 1 Q9ULT6 ZNRF3_HUMAN NP_115549 rs62641746 A/G 0.030762 0.120144 A>A>A -chr22:40814500 - MKL1 uc003ayv.1 ? CCDS14003.1 1 T/A missense 44939 A T CG 1 0 +123 -889 9/12 9/12 ? 0 648 0 AGC TGC S C 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc003ayv.1 ? CCDS14003.1 1 T/G missense 44939 A C CG 1 2 +123 -889 9/12 9/12 ? 0 648 0 AGC CGC S R 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc003ayw.1 16752 CCDS14003.1 1 T/A missense 218191 A T CG 1 0 +123 -889 12/15 9/12 ? 0 648 0 AGC TGC S C 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc003ayw.1 16752 CCDS14003.1 1 T/G missense 218191 A C CG 1 2 +123 -889 12/15 9/12 ? 0 648 0 AGC CGC S R 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc010gye.1 ? ? ? T/A missense 218191 A T CG 1 0 +123 -889 12/15 9/12 ? 0 648 0 AGC TGC S C 648 1 E7ER32 E7ER32_HUMAN ? ? ? ? ? ? -chr22:40814500 - MKL1 uc010gye.1 ? ? ? T/G missense 218191 A C CG 1 2 +123 -889 12/15 9/12 ? 0 648 0 AGC CGC S R 648 1 E7ER32 E7ER32_HUMAN ? ? ? ? ? ? -chr22:40814500 - MKL1 uc010gyf.1 ? ? ? T/A missense 218191 A T CG 1 0 +123 -889 11/14 8/11 ? 0 598 0 AGC TGC S C 598 1 B0QY83 B0QY83_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc010gyf.1 ? ? ? T/G missense 218191 A C CG 1 2 +123 -889 11/14 8/11 ? 0 598 0 AGC CGC S R 598 1 B0QY83 B0QY83_HUMAN NP_065882 ? ? ? ? ? -chr22:40815256 - MKL1 uc003ayv.1 ? CCDS14003.1 1 C/T missense 44183 G A CC 0 1 +879 -133 9/12 9/12 ? 0 396 0 GCC ACC A T 396 1 Q969V6 MKL1_HUMAN NP_065882 rs34736200 G/A 0.047299 0.14633 A>A>A -chr22:40815256 - MKL1 uc003ayw.1 16752 CCDS14003.1 1 C/T missense 217435 G A CC 0 1 +879 -133 12/15 9/12 ? 0 396 0 GCC ACC A T 396 1 Q969V6 MKL1_HUMAN NP_065882 rs34736200 G/A 0.047299 0.14633 A>A>A -chr22:40815256 - MKL1 uc010gye.1 ? ? ? C/T missense 217435 G A CC 0 1 +879 -133 12/15 9/12 ? 0 396 0 GCC ACC A T 396 1 E7ER32 E7ER32_HUMAN ? rs34736200 G/A 0.047299 0.14633 A>A>A -chr22:40815256 - MKL1 uc010gyf.1 ? ? ? C/T missense 217435 G A CC 0 1 +879 -133 11/14 8/11 ? 0 346 0 GCC ACC A T 346 1 B0QY83 B0QY83_HUMAN NP_065882 rs34736200 G/A 0.047299 0.14633 A>A>A -## Totals: -## lines input 4 -## lines skipped 0 -## alleles annotated 17 -## missense 17 -## nonsense 0 -## coding-synon 0 -## intron 0 -## utr-3 0 -## utr-5 0
--- a/mutationassesor_web/test-data/transfic_output.csv Tue Apr 15 12:21:30 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -#id location allele gene hgnc hgncdesc transcript ensp sw protein_position amino_acids uploaded_variation cdna_position cds_position codons existing_variation sift polyphen mass siftTransfic siftTransficLabel pph2Transfic pph2TransficLabel maTransfic maTransficLabel -19 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000428293 ENSP00000390734 NA 386 T/M 7_38471790_A 1226 1157 aCg/aTg COSM53413 0.01 0.998 NA 1.060 medium_impact 1.692 high_impact NA NA -17 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000447717 ENSP00000402803 NA 82 L/R 7_43918688_C 762 245 cTc/cGc COSM53414 0.05 0.995 NA 0.428 medium_impact 1.548 high_impact NA NA -18 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000546266 ENSP00000444695 NA 455 A/T 6_88372821_A 1720 1363 Gcc/Acc COSM53412 0.01 0.93 NA 1.183 medium_impact 1.186 medium_impact NA NA -15 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000392844 ENSP00000376586 ORC3_HUMAN 598 A/T 6_88372821_A 1840 1792 Gcc/Acc COSM53412 0.01 0.93 1.95 1.183 medium_impact 1.186 medium_impact 0.672 low_impact -16 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000452292 ENSP00000411130 NA 536 A/T 6_88372821_A 1615 1606 Gcc/Acc COSM53412 0.01 0.266 NA 1.183 medium_impact 0.241 medium_impact NA NA -13 5:41934236 G ENSG00000151876 FBXO4 F-box protein 4 ENST00000509134 ENSP00000421749 NA 242 K/E 5_41934236_G 733 724 Aag/Gag COSM53411 0.68 0.01 NA -1.057 low_impact -0.873 low_impact NA NA -14 5:41934236 G ENSG00000151876 FBXO4 F-box protein 4 ENST00000281623 ENSP00000281623 FBX4_HUMAN 242 K/E 5_41934236_G 780 724 Aag/Gag COSM53411 0.76 0.001 0 -1.222 low_impact -1.461 low_impact -1.088 low_impact -11 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000379882 ENSP00000369212 NA 598 L/F 9_32473058_A 1952 1794 ttA/ttT COSM53415 0.01 0.96 NA 1.138 medium_impact 1.048 medium_impact NA NA -12 5:41934236 G ENSG00000151876 FBXO4 F-box protein 4 ENST00000296812 ENSP00000296812 NA 242 K/E 5_41934236_G 780 724 Aag/Gag COSM53411 0.67 0.01 NA -1.039 low_impact -0.873 low_impact NA NA -21 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000353242 ENSP00000342268 NA 156 T/M 7_38471790_A 1226 467 aCg/aTg COSM53413 0 0.983 NA 1.935 medium_impact 1.177 medium_impact NA NA -20 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000356264 ENSP00000348602 AMPH_HUMAN 386 T/M 7_38471790_A 1373 1157 aCg/aTg COSM53413 0.01 0.998 1.79 1.060 medium_impact 1.692 high_impact 0.724 low_impact -22 6:88372821 A ENSG00000135336 ORC3 origin recognition complex, subunit 3 ENST00000257789 ENSP00000257789 NA 599 A/T 6_88372821_A 1829 1795 Gcc/Acc COSM53412 0.01 0.983 NA 1.183 medium_impact 1.572 high_impact NA NA -23 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000325590 ENSP00000317441 NA 386 T/M 7_38471790_A 1226 1157 aCg/aTg COSM53413 0.02 0.998 NA 0.794 medium_impact 1.692 high_impact NA NA -24 7:38471790 A ENSG00000078053 AMPH amphiphysin ENST00000441628 ENSP00000415085 NA 137 T/M 7_38471790_A 408 410 aCg/aTg COSM53413 0 0.983 NA 1.935 medium_impact 1.177 medium_impact NA NA -3 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000223341 ENSP00000223341 NA 82 L/R 7_43918688_C 622 245 cTc/cGc COSM53414 0.05 0.995 NA 0.428 medium_impact 1.548 high_impact NA NA -2 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000545044 ENSP00000443055 NA 440 L/F 9_32473058_A 1810 1320 ttA/ttT COSM53415 0 0.918 NA 2.043 high_impact 0.865 medium_impact NA NA -10 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000379883 ENSP00000369213 DDX58_HUMAN 643 L/F 9_32473058_A 2087 1929 ttA/ttT COSM53415 0.01 0.96 3.78 1.138 medium_impact 1.048 medium_impact 2.704 medium_impact -1 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000402306 ENSP00000384955 NA 116 L/R 7_43918688_C 387 347 cTc/cGc COSM53414 0.05 0.995 NA 0.428 medium_impact 1.548 high_impact NA NA -0 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000542096 ENSP00000442160 NA 572 L/F 9_32473058_A 2292 1716 ttA/ttT COSM53415 0.01 0.96 NA 1.138 medium_impact 1.048 medium_impact NA NA -7 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000453200 ENSP00000396918 URGCP_HUMAN 125 L/R 7_43918688_C 868 374 cTc/cGc COSM53414 0.05 0.995 2.545 0.428 medium_impact 1.548 high_impact 1.119 medium_impact -6 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000443736 ENSP00000392136 NA 82 L/R 7_43918688_C 420 245 cTc/cGc COSM53414 0.05 0.995 NA 0.428 medium_impact 1.548 high_impact NA NA -5 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000455877 ENSP00000392963 NA 82 L/R 7_43918688_C 469 245 cTc/cGc COSM53414 0 0.995 NA 1.969 medium_impact 1.548 high_impact NA NA -4 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000426198 ENSP00000389990 NA 82 L/R 7_43918688_C 640 245 cTc/cGc COSM53414 0.09 0.995 NA 0.183 medium_impact 1.548 high_impact NA NA -9 9:32473058 A ENSG00000107201 DDX58 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 ENST00000379868 ENSP00000369197 NA 440 L/F 9_32473058_A 1823 1320 ttA/ttT COSM53415 0.01 0.96 NA 1.138 medium_impact 1.048 medium_impact NA NA -8 7:43918688 C ENSG00000106608 URGCP upregulator of cell proliferation ENST00000336086 ENSP00000336872 NA 82 L/R 7_43918688_C 2482 245 cTc/cGc COSM53414 0.05 0.995 NA 0.428 medium_impact 1.548 high_impact NA NA