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comparison cravat_submit/Z_Additional_Details2018-08-16_15-00-12_.tsv @ 19:275d45d14350 draft

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author in_silico
date Thu, 16 Aug 2018 15:10:07 -0400
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18:25f77adaf9d9 19:275d45d14350
1 #Variant Additional Details Report
2 #2018-08-16 19:00:07.742990
3 #CRAVAT version: hybrid
4 #Analysis done at http://www.cravat.us.
5 #Job Id: cravatgalaxy_20180816_145959
6 #Input file: converted.txt
7 #This report shows analysis results at variant level.
8 #hg38 genomic.
9 #N/A
10 #For more information on CRAVAT, visit http://www.cravat.us.
11
12 Input line ID Chromosome Position Strand Reference base(s) Alternate base(s) Sample ID HUGO symbol Sequence ontology S.O. transcript S.O. transcript strand Protein sequence change S.O. all transcripts CGC driver class CGC inheritance CGC tumor types somatic CGC tumor types germline ClinVar disease identifier ClinVar XRef COSMIC transcript COSMIC protein change COSMIC variant count ESP6500 AF (European American) ESP6500 AF (African American) HGVS Genomic HGVS Protein HGVS Protein All NCI pathway hits NCI pathway IDs NCI pathway names VEST score transcript VEST p-value VEST score (missense) VEST score (frameshift indels) VEST score (inframe indels) VEST score (stop-gain) VEST score (stop-loss) VEST score (splice site) All transcripts VEST results
13 1 TR1 chr22 30025797 + A T sample_1 MTMR3 MS ENST00000401950.6 + N1198I ENST00000323630.9:N1062I(MS),ENST00000351488.7:N1161I(MS),ENST00000333027.7:N1170I(MS),ENST00000406629.1:N1170I(MS),*ENST00000401950.6:N1198I(MS) 0 0.0226963 NC_000022.10:g.30025797A>T ENST00000401950.6:p.Asn1198Ile ENST00000323630.9:p.Asn1062Ile,ENST00000351488.7:p.Asn1161Ile,ENST00000333027.7:p.Asn1170Ile,ENST00000406629.1:p.Asn1170Ile,*ENST00000401950.6:p.Asn1198Ile 0 ENST00000323630.9:N1062I 0.14523 0.569 ENST00000401950.6:N1198I(0.5:0.18672),ENST00000333027.7:N1170I(0.475:0.19897),*ENST00000323630.9:N1062I(0.569:0.14523),ENST00000406629.1:N1170I(0.466:0.20362),ENST00000351488.7:N1161I(0.482:0.19512)
14 2 TR2 chr22 40418496 - A G sample_1 MKL1 MS ENST00000618196.4 - S683G ENST00000396617.7:S648G(MS),ENST00000614754.4:S649G(MS),ENST00000402042.5:S598G(MS),ENST00000620651.4:S599G(MS),ENST00000407029.5:S648G(MS),ENST00000355630.7:S648G(MS),*ENST00000618196.4:S683G(MS) somatic acute megakaryocytic leukaemia ENST00000355630 p.S648G (stomach 1) 1 0.396977 0.860645 NC_000022.10:g.40418496T>C ENST00000618196.4:p.Ser683Gly ENST00000396617.7:p.Ser648Gly,ENST00000614754.4:p.Ser649Gly,ENST00000402042.5:p.Ser598Gly,ENST00000620651.4:p.Ser599Gly,ENST00000407029.5:p.Ser648Gly,ENST00000355630.7:p.Ser648Gly,*ENST00000618196.4:p.Ser683Gly 1 5d9755d6-5521-11e7-8f50-0ac135e8bacf RhoA signaling pathway ENST00000620651.4:S599G 0.77158 0.104 ENST00000396617.7:S648G(0.057:0.92622),ENST00000355630.7:S648G(0.04:0.96174),ENST00000407029.5:S648G(0.043:0.95567),*ENST00000620651.4:S599G(0.104:0.77158),ENST00000618196.4:S683G(0.037:0.9662),ENST00000614754.4:S649G(0.062:0.91296),ENST00000402042.5:S598G(0.093:0.80893)
15 3 TR3 chr22 40419252 + C T sample_1 MKL1 MS ENST00000618196.4 - A431T ENST00000396617.7:A396T(MS),ENST00000614754.4:A397T(MS),ENST00000402042.5:A346T(MS),ENST00000620651.4:A347T(MS),ENST00000407029.5:A396T(MS),ENST00000355630.7:A396T(MS),*ENST00000618196.4:A431T(MS) somatic acute megakaryocytic leukaemia 0.00127937 0.0834091 NC_000022.10:g.40419252C>T ENST00000618196.4:p.Ala431Thr ENST00000396617.7:p.Ala396Thr,ENST00000614754.4:p.Ala397Thr,ENST00000402042.5:p.Ala346Thr,ENST00000620651.4:p.Ala347Thr,ENST00000407029.5:p.Ala396Thr,ENST00000355630.7:p.Ala396Thr,*ENST00000618196.4:p.Ala431Thr 1 5d9755d6-5521-11e7-8f50-0ac135e8bacf RhoA signaling pathway ENST00000620651.4:A347T 0.80893 0.093 ENST00000396617.7:A396T(0.039:0.96377),ENST00000355630.7:A396T(0.039:0.96377),ENST00000407029.5:A396T(0.033:0.97116),*ENST00000620651.4:A347T(0.093:0.80893),ENST00000618196.4:A431T(0.034:0.97045),ENST00000614754.4:A397T(0.029:0.97723),ENST00000402042.5:A346T(0.042:0.95749)
16 4 TR4 chr22 24719483 + - AGG sample_2 PIWIL3 II ENST00000332271.9 - F880SF ENST00000533313.5:F762SF(II),ENST00000527701.5:F762SF(II),*ENST00000332271.9:F880SF(II),ENST00000616349.4:F880SF(II) 0 0 NC_000022.10:g.24719482_24719483insAGG ENST00000332271.9:p.Leu879_Phe880insSer ENST00000533313.5:p.Leu761_Phe762insSer,ENST00000527701.5:p.Leu761_Phe762insSer,*ENST00000332271.9:p.Leu879_Phe880insSer,ENST00000616349.4:p.Leu879_Phe880insSer 0 ENST00000533313.5:762 0.47384 0.14 *ENST00000533313.5:762(0.14:0.47384),ENST00000332271.9:880(0.12:0.5116),ENST00000527701.5:762(0.14:0.47384),ENST00000616349.4:880(0.11:0.53414)