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annotate chasm_webservice/test-data/chasm_output_variants.tabular @ 9:473d1c2ca65d draft default tip

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author saketkc
date Tue, 07 Oct 2014 18:32:57 -0400
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1 #Variant Level Analysis Report
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2 #2014-08-28 22:54:22.488508
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3 #CRAVAT version: 3.1
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4 #Analysis done at http://www.cravat.us.
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5 #Input file: dataset_1.dat
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6 #This report shows analysis results at variant level.
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7 #Input coordinate was hg19 genomic.
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8 #Tissue type for CHASM analysis: Other
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9 #For more information on CRAVAT, visit http://www.cravat.us.
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10 #
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11 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) Protein sequence change Other transcripts Mappability Warning Driver Genes TARGET 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 in COSMIC Protein sequence change in COSMIC Occurrences in COSMIC [exact nucleotide change] Occurrences in COSMIC by primary sites [exact nucleotide change] MuPIT Link
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12 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 0.582(NM_021090.3:N1198I:&) 0.2972 0.572(ENST00000351488:N1161I:=) ENST00000323630:N1062I:=(0.594),ENST00000406629:N1170I:=(0.602),ENST00000401950:N1198I:=(0.592),ENST00000351488:N1161I:=(0.572),NM_153050.2:N1170I:=(0.582),ENST00000333027:N1170I:=(0.582),NM_021090.3:N1198I:&(0.582),NM_153051.2:N1161I:=(0.582) rs75623810 0.00778388278388 0 0.0226963 1
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13 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 0.524(NM_001206998.1:H637R:&) 0.1872 0.442(ENST00000544604:H637R:=) ENST00000544604:H637R:=(0.442),NM_032173.3:H537R:=(0.524),ENST00000402174:H537R:=(0.524),ENST00000406323:H537R:=(0.514),NM_001206998.1:H637R:&(0.524),ENST00000332811:H537R:=(0.524) rs62641746 0 0.00598145 0.00104004 2
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14 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 0.524(NM_001206998.1:H637R:&) 0.1872 0.442(ENST00000544604:H637R:=) ENST00000544604:H637R:=(0.442),NM_032173.3:H537R:=(0.524),ENST00000402174:H537R:=(0.524),ENST00000406323:H537R:=(0.514),NM_001206998.1:H637R:&(0.524),ENST00000332811:H537R:=(0.524) rs62641746 0 0.00598145 0.00104004 2
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15 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 0.704(ENST00000402042:S598G:=) ENST00000407029:S648G:=(0.728),NM_020831.3:S648G:&(0.728),ENST00000396617:S648G:=(0.728),ENST00000355630:S648G:=(0.728),ENST00000402042:S598G:=(0.704) rs878756 0.419871794872 0.396977 0.860645 1 ENST00000355630 p.S648G (stomach 1) 1 stomach(1)
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16 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 0.668(NM_020831.3:A396T:&) 0.5102 0.668(ENST00000407029:A396T:=) ENST00000407029:A396T:=(0.668),NM_020831.3:A396T:&(0.668),ENST00000396617:A396T:=(0.668),ENST00000355630:A396T:=(0.668),ENST00000402042:A346T:=(0.67) rs34736200 0.0201465201465 0.00127937 0.0834091 1