annotate test-data/rif_resistant_variants_report_with_lineage.txt @ 4:9793bc5d741b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit a8fe4cf3a77ffb0334533cccb57b7af5f7f89e3b

#Rif_resistant Report
#Lineage	Support	Family	RD
lineage2	0.9940119760479041	East-Asian	RD105
lineage2.2.2	1.0	East-Asian (Beijing)	RD105;RD207

#CHR	GENE	IDENTIFIER	PRODUCT	IS_SNV	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHWAY
Chromosome	Rv0014c	GENE_Rv0014c	NOPROTEIN	True	synonymous_variant	15890	G	A	p.Ser527Ser	LOW	
Chromosome	Rv0127	GENE_Rv0127	NOPROTEIN	True	synonymous_variant	154990	G	T	p.Arg253Arg	LOW	
Chromosome	Rv0284	GENE_Rv0284	NOPROTEIN	True	synonymous_variant	346693	G	T	p.Ser353Ser	LOW	
Chromosome	Rv0372c	GENE_Rv0372c	NOPROTEIN	True	synonymous_variant	449194	G	A	p.Gly64Gly	LOW	
Chromosome	Rv0411c	GENE_Rv0411c	NOPROTEIN	True	synonymous_variant	497491	G	A	p.Asp270Asp	LOW	
Chromosome	Rv0667	GENE_Rv0667	NOPROTEIN	True	missense_variant	761110	A	T	p.Asp435Val	MODERATE	
Chromosome	Rv0715	GENE_Rv0715	NOPROTEIN	True	synonymous_variant	811753	C	T	p.His4His	LOW	
Chromosome	Rv1391	GENE_Rv1391	NOPROTEIN	True	synonymous_variant	1565566	C	T	p.Pro42Pro	LOW	
Chromosome	Rv1630	GENE_Rv1630	NOPROTEIN	True	synonymous_variant	1834177	A	C	p.Arg212Arg	LOW	
Chromosome	Rv1640c	GENE_Rv1640c	NOPROTEIN	True	synonymous_variant	1849051	C	T	p.Pro995Pro	LOW	
Chromosome	Rv2231c	GENE_Rv2231c	NOPROTEIN	True	synonymous_variant	2505085	G	A	p.Ala205Ala	LOW	
Chromosome	Rv2268c	GENE_Rv2268c	NOPROTEIN	True	synonymous_variant	2543395	T	C	p.Glu294Glu	LOW	
Chromosome	Rv2357c	GENE_Rv2357c	NOPROTEIN	True	synonymous_variant	2640807	G	A	p.Val86Val	LOW	
Chromosome	Rv2472	GENE_Rv2472	NOPROTEIN	True	synonymous_variant	2775361	C	T	p.Arg30Arg	LOW	
Chromosome	Rv2483c	GENE_Rv2483c	NOPROTEIN	True	synonymous_variant	2789798	G	T	p.Arg409Arg	LOW	
Chromosome	Rv3109	GENE_Rv3109	NOPROTEIN	True	synonymous_variant	3477942	A	G	p.Thr98Thr	LOW	
Chromosome	Rv3210c	GENE_Rv3210c	NOPROTEIN	True	synonymous_variant	3587446	G	A	p.Leu32Leu	LOW	
Chromosome	Rv3799c	GENE_Rv3799c	NOPROTEIN	True	synonymous_variant	4254431	G	A	p.Asp506Asp	LOW	
Chromosome	Rv3799c	GENE_Rv3799c	NOPROTEIN	True	missense_variant	4254477	T	C	p.His491Arg	MODERATE