view cravat_submit/Z_Variant_Result2018-08-16_15-00-12_.tsv @ 19:275d45d14350 draft

author in_silico
date Thu, 16 Aug 2018 15:10:07 -0400
parents 9985359fa7ff
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#Variant Report
#2018-08-16 19:00:07.740432
#CRAVAT version: hybrid
#Analysis done at
#Job Id: cravatgalaxy_20180816_145959
#Input file: converted.txt
#This report shows analysis results at variant level.
#hg38 genomic.
#For more information on CRAVAT, visit

Input line	ID	Chromosome	Position	Strand	Reference base(s)	Alternate base(s)	Sample ID	HUGO symbol	Sequence ontology	Protein sequence change	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	VEST p-value	VEST FDR	CGL driver class
1	TR1	chr22	30025797	+	A	T	sample_1	MTMR3	MS	N1198I				1	rs75623810	0.01134815	0.00229508433352	0.0250541035459	0.000900691498634				1.57942951006e-05	0.00015475085113															0.00778754				0.14523		
2	TR2	chr22	40418496	-	A	G	sample_1	MKL1	MS	S683G		COSM149301	stomach(1)	1	rs878756	0.628811																							0.483227	intron	MKL1	ENST00000618417.1(intron)	0.77158		
3	TR3	chr22	40419252	+	C	T	sample_1	MKL1	MS	A431T				1	rs34736200	0.042344235	0.00952521054761	0.092516658124	0.00484894792524	0.00298626318933	0.00198817839871		0.000953211839214	0.00409191060749	0.00158217417101				../MuPIT_Interactive?gm=chr22:40419252										0.0279553	intron	MKL1	ENST00000618417.1(intron)	0.80893		
4	TR4	chr22	24719483	+	-	AGG	sample_2	PIWIL3	II	F880SF				1		0.0													../MuPIT_Interactive?gm=chr22:24719483										0				0.47384