TB-Profiler result

Run: SRR6485165
Summary

Run ID: SRR6485165

Sample name:

Date: 04-04-2023 15:13:27

Number of reads: 1583037

Percentage reads mapped: 99.49

Strain: lineage4.2.1.1

Drug-resistance: MDR-TB

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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776802 p.Met560Thr missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475050 n.1393A>T non_coding_transcript_exon_variant 0.5
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
tlyA 1917770 c.-170T>A upstream_gene_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167651 c.2962T>A stop_lost&splice_region_variant 0.29
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.38
PPE35 2170392 p.Gly74Ala missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714758 p.Arg192Leu missense_variant 0.14
Rv2752c 3065901 c.291A>C synonymous_variant 0.18
Rv2752c 3065958 c.234G>A synonymous_variant 1.0
thyX 3067266 p.Phe227Tyr missense_variant 0.12
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642562 p.Asp343Ala missense_variant 0.12
ddn 3987092 p.Glu83Asp missense_variant 1.0
clpC1 4040605 p.Leu34Ile missense_variant 0.17
clpC1 4040786 c.-82G>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0