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view test-results/combined_variants.tsv @ 0:83181dabeb90 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
| author | galaxyp |
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| date | Fri, 18 May 2018 13:25:29 -0400 |
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#Variant Additional Details Report #2018-05-18 15:15:25.120629 #CRAVAT version: hybrid #Analysis done at http://www.cravat.us. #Job Id: znylund_20180518_111521 #Input file: _VCF_BEDintersect_on_data_65_and_data_6_.vcf #This report shows analysis results at variant level. #hg38 genomic. #N/A #For more information on CRAVAT, visit http://www.cravat.us. 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 Reference peptide Variant peptide 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 ClinVar COSMIC ID COSMIC variant count (tissue) Number of samples with variant dbSNP ESP6500 AF (average) gnomAD AF Total gnomAD AF African gnomAD AF American gnomAD AF Ashkenazi Jewish gnomAD AF East Asian gnomAD AF Finnish gnomAD AF Non-Finnish European gnomAD AF Other gnomAD AF South Asian GWAS NHLBI Key (GRASP) GWAS PMID (GRASP) GWAS Phenotype (GRASP) Protein 3D variant In TCGA Mutation Cluster ncRNA Class ncRNA Name Pseudogene Pseudogene Transcript Repeat Class Repeat Family Repeat Name TARGET 1000 Genomes AF UTR/Intron UTR/Intron Gene UTR/Intron All Transcript Phred VCF filters Zygosity Alternate reads Total reads Variant allele frequency VEST FDR CGL driver class 1 VAR516_unknown chr1 156705422 + T C unknown CRABP2 MS ENST00000368221.1 - MPNFSGNWKIIR MPNFSGNWEIIR K9E *ENST00000368221.1:K9E(MS),ENST00000621784.4:K9E(MS),ENST00000368222.7:K9E(MS) ENST00000368221 p.K9E (large_intestine 1) 1 0 0 NC_000001.10:g.156705422T>C ENST00000368221.1:p.Lys9Glu *ENST00000368221.1:p.Lys9Glu,ENST00000621784.4:p.Lys9Glu,ENST00000368222.7:p.Lys9Glu 0 ENST00000368221.1:K9E 0.53061 0.2 *ENST00000368221.1:K9E(0.2:0.53061),ENST00000368222.7:K9E(0.187:0.5543),ENST00000621784.4:K9E(0.186:0.55652) COSM1984142 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr1:156705422 0 125181 . het 5739 18018 0.318514818515 2 VAR517_unknown chr12 6561055 + T C unknown NOP2 MS ENST00000616948.4 - NTGVILANDANAER STGVILANDANAER N408S ENST00000617555.4:N404S(MS),ENST00000545200.5:N404S(MS),ENST00000541778.5:N404S(MS),ENST00000399466.6:N404S(MS),ENST00000322166.9:N408S(MS),ENST00000537442.5:N408S(MS),ENST00000382421.7:N441S(MS),ENST00000620535.4:N441S(MS),*ENST00000616948.4:N408S(MS) 0 0 NC_000012.10:g.6561055T>C ENST00000616948.4:p.Asn408Ser ENST00000617555.4:p.Asn404Ser,ENST00000545200.5:p.Asn404Ser,ENST00000541778.5:p.Asn404Ser,ENST00000399466.6:p.Asn404Ser,ENST00000322166.9:p.Asn408Ser,ENST00000537442.5:p.Asn408Ser,ENST00000382421.7:p.Asn441Ser,ENST00000620535.4:p.Asn441Ser,*ENST00000616948.4:p.Asn408Ser 0 ENST00000616948.4:N408S 0.00324 0.958 ENST00000617555.4:N404S(0.954:0.00354),*ENST00000616948.4:N408S(0.958:0.00324),ENST00000541778.5:N404S(0.869:0.01488),ENST00000537442.5:N408S(0.956:0.00344),ENST00000399466.6:N404S(0.951:0.00374),ENST00000545200.5:N404S(0.953:0.00354),ENST00000620535.4:N441S(0.938:0.00536),ENST00000382421.7:N441S(0.938:0.00536),ENST00000322166.9:N408S(0.954:0.00354) 1 0.0 ../MuPIT_Interactive?gm=chr12:6561055 0 14340.8 . het 910 3868 0.235263702172 3 VAR518_unknown chr12 110339630 + C T unknown ATP2A2 MS ENST00000539276.6 + EWGSGSDTLR EWGSGSDILR T557I ENST00000308664.10:T557I(MS),*ENST00000539276.6:T557I(MS) 0 0 NC_000012.10:g.110339630C>T ENST00000539276.6:p.Thr557Ile ENST00000308664.10:p.Thr557Ile,*ENST00000539276.6:p.Thr557Ile 0 ENST00000539276.6:T557I 0.00374 0.951 ENST00000308664.10:T557I(0.822:0.02459),*ENST00000539276.6:T557I(0.951:0.00374) 1 0.0 ../MuPIT_Interactive?gm=chr12:110339630 0 48828.1 . het 2447 9100 0.268901098901 4 VAR520_unknown chr14 102011985 + A T unknown DYNC1H1 MS ENST00000360184.8 + ALERLEGVEGVAHIIDPK ALESLEGVEGVAHIIDPK R2243S *ENST00000360184.8:R2243S(MS) ENST00000360184 p.R2243S (large_intestine 1) 1 0 0 NC_000014.10:g.102011985A>T ENST00000360184.8:p.Arg2243Ser *ENST00000360184.8:p.Arg2243Ser 1 94da5dd8-5521-11e7-8f50-0ac135e8bacf Lissencephaly gene (LIS1) in neuronal migration and development ENST00000360184.8:R2243S 0.02307 0.829 *ENST00000360184.8:R2243S(0.829:0.02307) COSM2262213 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr14:102011985 0 12962.3 . het 642 2131 0.301267010793 5 VAR521_unknown chr14 102083954 + C T unknown HSP90AA1 MS ENST00000334701.11 - GVVDSEDLPLNISR GVVDSENLPLNISR D515N ENST00000216281.12:D393N(MS),*ENST00000334701.11:D515N(MS) somatic NHL ENST00000334701 p.D515N (large_intestine 1) 1 0 0 NC_000014.10:g.102083954C>T ENST00000334701.11:p.Asp515Asn ENST00000216281.12:p.Asp393Asn,*ENST00000334701.11:p.Asp515Asn 15 3814fa62-5521-11e7-8f50-0ac135e8bacf,32ff1916-5521-11e7-8f50-0ac135e8bacf,a8411a5c-5521-11e7-8f50-0ac135e8bacf,541d7e20-5521-11e7-8f50-0ac135e8bacf,98ad85f0-5521-11e7-8f50-0ac135e8bacf,9697501e-5521-11e7-8f50-0ac135e8bacf,e6f69242-5521-11e7-8f50-0ac135e8bacf,603902ca-5521-11e7-8f50-0ac135e8bacf,bb3d7c4a-5521-11e7-8f50-0ac135e8bacf,b1ac7318-5521-11e7-8f50-0ac135e8bacf,cb348d72-5521-11e7-8f50-0ac135e8bacf,945aa686-5521-11e7-8f50-0ac135e8bacf,4c90f780-5521-11e7-8f50-0ac135e8bacf,e4e93610-5521-11e7-8f50-0ac135e8bacf,6f7a316e-5521-11e7-8f50-0ac135e8bacf Validated targets of C-MYC transcriptional activation@VEGFR1 specific signals@IL2 signaling events mediated by PI3K@Signaling events mediated by HDAC Class II@Integrin-linked kinase signaling@Integrins in angiogenesis@Class I PI3K signaling events mediated by Akt@Regulation of Telomerase@Glucocorticoid receptor regulatory network@Hypoxic and oxygen homeostasis regulation of HIF-1-alpha@ErbB receptor signaling network@LKB1 signaling events@Signaling events mediated by VEGFR1 and VEGFR2@Class I PI3K signaling events@Regulation of Androgen receptor activity ENST00000216281.12:D393N 0.02014 0.84 ENST00000334701.11:D515N(0.749:0.04989),*ENST00000216281.12:D393N(0.84:0.02014) COSM2262393 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr14:102083954 0 240809 . het 17374 85275 0.203740838464 6 VAR522_unknown chr17 82082606 + C T unknown FASN MS ENST00000306749.3 - QGVQVQVSTSNISSLEGAR QGVQVQVSTSNINSLEGAR S1947N ENST00000634990.1:S1945N(MS),*ENST00000306749.3:S1947N(MS) ENST00000306749 p.S1947N (large_intestine 1) 1 0 0 NC_000017.10:g.82082606C>T ENST00000306749.3:p.Ser1947Asn ENST00000634990.1:p.Ser1945Asn,*ENST00000306749.3:p.Ser1947Asn 2 34a994cc-5521-11e7-8f50-0ac135e8bacf,812903c2-5521-11e7-8f50-0ac135e8bacf Validated transcriptional targets of deltaNp63 isoforms@p73 transcription factor network ENST00000634990.1:S1945N 0.18611 0.501 ENST00000306749.3:S1947N(0.493:0.19016),*ENST00000634990.1:S1945N(0.501:0.18611) COSM4648107 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr17:82082606 0 10374.8 . het 776 3826 0.202822791427 7 VAR523_unknown chr19 17205335 + A T unknown MYO9B MS ENST00000594824.5 + IQSHCSYTYGRKGEPGVEPGHFGVCVDSLTSDK IQSHCSYTYGRMGEPGAEPGHFGVCVDSLTSDK K1688M ENST00000397274.6:K1688M(MS),ENST00000595618.5:K1688M(MS),*ENST00000594824.5:K1688M(MS) 0 0 NC_000019.10:g.17205335A>T ENST00000594824.5:p.Lys1688Met ENST00000397274.6:p.Lys1688Met,ENST00000595618.5:p.Lys1688Met,*ENST00000594824.5:p.Lys1688Met 1 60f3521c-5521-11e7-8f50-0ac135e8bacf Regulation of RhoA activity ENST00000397274.6:K1688M 0.20028 0.473 ENST00000594824.5:K1688M(0.464:0.20464),*ENST00000397274.6:K1688M(0.473:0.20028),ENST00000595618.5:K1688M(0.469:0.20231) 1 0.0 ../MuPIT_Interactive?gm=chr19:17205335 0 0.00158993 . het 2 7 0.285714285714 9 VAR525_unknown chr19 17205973 + T C unknown MYO9B MS ENST00000594824.5 + IQSHCSYTYGRKGEPGVEPGHFGVCVDSLTSDK IQSHCSYTYGRMGEPGAEPGHFGVCVDSLTSDK V1693A ENST00000397274.6:V1693A(MS),ENST00000595618.5:V1693A(MS),*ENST00000594824.5:V1693A(MS) ENST00000319396 p.V1693A (thyroid 2) 2 0.399857 0.645631 NC_000019.10:g.17205973T>C ENST00000594824.5:p.Val1693Ala ENST00000397274.6:p.Val1693Ala,ENST00000595618.5:p.Val1693Ala,*ENST00000594824.5:p.Val1693Ala 1 60f3521c-5521-11e7-8f50-0ac135e8bacf Regulation of RhoA activity ENST00000397274.6:V1693A 0.95254 0.045 ENST00000594824.5:V1693A(0.025:0.98158),*ENST00000397274.6:V1693A(0.045:0.95254),ENST00000595618.5:V1693A(0.042:0.95749) COSM438878 thyroid(2) 1 rs7248508 0.522744 0.526958747465 0.685404424473 0.728029336735 0.352247807018 0.776672496721 0.453231381586 0.406255640183 0.486462728551 0.596900776808 190609063506732,203395363506733,206865653506734,208819603506735,224846277709335,224792027709336 19060906,20339536,20686565,20881960,22484627,22479202 LDL cholesterol(0.0152),HDL cholesterol(0.0279),Triglycerides(0.0141),Height(0.0104),Obesity with early age of onset (age >2)(0.0471),Adiponectin levels(0.0294) ../MuPIT_Interactive?gm=chr19:17205973 0.631589 12243.8 . hom 812 406 2.0 10 VAR526_unknown chr19 18856059 + C T unknown UPF1 MS ENST00000599848.5 + EAIDSPVSFLALHNQIR EAIDSPVSFLVLHNQIR A571V ENST00000262803.9:A560V(MS),*ENST00000599848.5:A571V(MS) ENST00000262803 p.A560V (large_intestine 1) 1 0 0 NC_000019.10:g.18856059C>T ENST00000599848.5:p.Ala571Val ENST00000262803.9:p.Ala560Val,*ENST00000599848.5:p.Ala571Val 0 ENST00000262803.9:A560V 0.09372 0.662 ENST00000599848.5:A571V(0.643:0.10292),*ENST00000262803.9:A560V(0.662:0.09372) COSM3100527 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr19:18856059 0 10269.5 . het 592 2379 0.248844052123