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

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#Variant Additional Details Report
#2018-08-16 19:00:07.742990
#CRAVAT version: hybrid
#Analysis done at http://www.cravat.us.
#Job Id: cravatgalaxy_20180816_145959
#Input file: converted.txt
#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	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
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)
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)
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)
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)