TB-Profiler result

Run: ERR2229229

Summary

Run ID: ERR2229229

Sample name:

Date: 31-03-2023 16:50:04

Number of reads: 478794

Percentage reads mapped: 98.83

Strain: lineage4.8

Drug-resistance: Sensitive


Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8941 c.1644delG frameshift_variant 0.14
mshA 575729 p.Gln128Lys missense_variant 0.33
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoB 760619 c.813C>A synonymous_variant 0.4
rpoB 761409 p.Val535Leu missense_variant 0.2
rpoC 764826 p.Val486Ala missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776420 c.2061C>T synonymous_variant 0.5
mmpL5 777614 c.867C>T synonymous_variant 0.29
mmpL5 777658 p.Thr275Pro missense_variant 0.4
mmpL5 777966 p.Ile172Asn missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304715 c.1785G>C synonymous_variant 0.18
fbiC 1305389 p.Ala820Val missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475305 n.1648A>G non_coding_transcript_exon_variant 0.4
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
rpsA 1833666 p.Thr42Ser missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918191 c.252G>A synonymous_variant 0.4
katG 2155344 c.768C>T synonymous_variant 0.29
katG 2155990 p.Asn41Ser missense_variant 0.22
PPE35 2167833 p.Leu927Arg missense_variant 0.18
PPE35 2167965 p.Ala883Gly missense_variant 0.19
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2168329 p.Pro762Thr missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169570 p.Ser348Asn missense_variant 0.12
PPE35 2169578 c.1035T>C synonymous_variant 0.12
PPE35 2169638 c.975T>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.39
PPE35 2170147 p.Ser156Ala missense_variant 0.18
PPE35 2170220 c.393C>G synonymous_variant 0.22
PPE35 2170229 c.384A>G synonymous_variant 0.15
PPE35 2170232 c.381T>A synonymous_variant 0.14
PPE35 2170238 c.375T>G synonymous_variant 0.14
PPE35 2170247 p.Ile122Met missense_variant 0.16
PPE35 2170259 p.Ile118Met missense_variant 0.15
PPE35 2170372 p.Thr81Ala missense_variant 0.12
PPE35 2170376 c.237G>A synonymous_variant 0.12
PPE35 2170454 c.159C>G synonymous_variant 0.18
PPE35 2170528 p.Ser29Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288785 p.Thr153Ser missense_variant 0.2
pncA 2288793 p.Gly150Asp missense_variant 0.17
kasA 2518317 p.Val68Ala missense_variant 0.2
eis 2715268 p.Ala22Asp missense_variant 0.13
pepQ 2860414 p.Thr2Ile missense_variant 0.33
Rv2752c 3065104 p.Val363Ala missense_variant 0.22
thyX 3068011 c.-66C>T upstream_gene_variant 0.29
thyX 3068015 c.-70T>G upstream_gene_variant 0.29
thyA 3074217 p.Ser85Arg missense_variant 0.5
fbiA 3640681 p.Val47Phe missense_variant 0.12
fbiB 3641697 p.Lys55Glu missense_variant 0.17
fbiB 3642621 p.Ala363Thr missense_variant 0.18
alr 3840670 p.Val251Leu missense_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.2
rpoA 3878164 p.Gly115Val missense_variant 0.14
ddn 3986728 c.-116T>A upstream_gene_variant 0.14
clpC1 4040340 c.364delC frameshift_variant 0.2
embC 4240353 p.Val164Gly missense_variant 0.5
embC 4241220 p.Ile453Ser missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244082 p.Ala284Thr missense_variant 0.15
embB 4245923 c.-591C>A upstream_gene_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4248310 c.1797C>T synonymous_variant 0.29
embB 4248707 p.Thr732Pro missense_variant 0.29
ubiA 4269017 p.Glu273* stop_gained 0.17
ethA 4327504 c.-31G>C upstream_gene_variant 0.25
whiB6 4338373 p.Lys50Arg missense_variant 0.2
whiB6 4338418 p.Thr35Met missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0