annotate test-data/vcf_with_no_protein_report.txt @ 3:42818629ec4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17

#Vcf_with_no_protein Report

#CHR	GENE	IDENTIFIER	PRODUCT	IS_SNV	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHWAY
Chromosome	Rv3753c	Rv3753c	O69720	True	missense_variant	4200220	G	A	p.Thr1Met	MODERATE	
Chromosome	Rv3756c	Rv3756c	O69722	True	synonymous_variant	4202383	C	A	p.Val77Val	LOW	ABC transporters
Chromosome	Rv3759c	Rv3759c	O69725	True	missense_variant	4205120	G	A	p.Pro85Leu	MODERATE	ABC transporters
Chromosome	Rv3764c	Rv3764c	O69729	True	missense_variant	4210876	C	T	p.Arg45His	MODERATE	
Chromosome	Rv3769	Rv3769	P72036	True	missense_variant	4214747	C	T	p.His45Tyr	MODERATE	
Chromosome	Rv3770c	Rv3770c	P72037	True	missense_variant	4215484	C	G	p.Ala98Pro	MODERATE	
Chromosome	Rv3772	Rv3772	P9WML5	True	missense_variant	4217557	G	A	p.Ala142Thr	MODERATE	Phenylalanine, tyrosine and tryptophan biosynthesis,Phenylalanine metabolism,Histidine metabolism,Tyrosine metabolism
Chromosome	Rv3777	Rv3777	P72043	True	missense_variant	4223172	C	T	p.Ala160Val	MODERATE	
Chromosome	Rv3785	Rv3785	P9WKX1	True	synonymous_variant	4232327	G	A	p.Arg336Arg	LOW	
Chromosome	Rv3792	Rv3792	P9WN03	True	synonymous_variant	4238963	C	T	p.His344His	LOW	Arabinogalactan biosynthesis - Mycobacterium
Chromosome	Rv3792	Rv3792	P9WN03	True	missense_variant	4239274	C	G	p.Pro448Arg	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
Chromosome	Rv3793	Rv3793	P9WNL5	True	missense_variant	4240671	T	C	p.Ile270Thr	MODERATE	Lipoarabinomannan (LAM) biosynthesis
Chromosome	Rv3795	Rv3795	P9WNL7	True	missense_variant	4247429	A	G	p.Met306Val	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
Chromosome	Rv3795	Rv3795	P9WNL7	True	missense_variant	4247646	C	A	p.Ala378Glu	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
Chromosome	Rv3797	Rv3797	O53577	True	synonymous_variant	4251297	C	G	p.Gly71Gly	LOW	
Chromosome	Rv3798	Rv3798	NOPROTEIN	True	missense_variant	4254290	T	G	p.Leu433Arg	MODERATE	
Chromosome	Rv3799c	Rv3799c	O53578	True	missense_variant	4254478	G	A	p.His491Tyr	MODERATE	
Chromosome	Rv3801c	Rv3801c	O53580	True	missense_variant	4261499	A	G	p.Val523Ala	MODERATE