TB-Profiler result

Run: SRR22528549
Summary

Run ID: SRR22528549

Sample name:

Date: 04-04-2023 04:18:32

Number of reads: 1817984

Percentage reads mapped: 99.66

Strain: lineage4.3.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrB 6755 p.Ile506Phe missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761528 p.Asp574Glu missense_variant 1.0
rpoB 761895 p.Ala697Ser missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406783 c.558C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
fabG1 1673608 p.Gly57Cys missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223089 p.Ser26Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860113 c.306C>G synonymous_variant 0.11
pepQ 2860120 p.His100Pro missense_variant 0.18
pepQ 2860131 c.288C>G synonymous_variant 0.11
pepQ 2860140 c.279A>T synonymous_variant 0.13
pepQ 2860144 p.Val92Gly missense_variant 0.2
pepQ 2860148 p.Gly91Arg missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087846 p.Leu343Val missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.2
whiB7 3568441 p.Lys80Thr missense_variant 0.15
rpoA 3877557 c.951C>G synonymous_variant 0.33
rpoA 3878653 c.-146A>C upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040262 p.Lys148Thr missense_variant 0.11
clpC1 4040874 c.-170C>G upstream_gene_variant 0.11
clpC1 4040886 c.-182T>G upstream_gene_variant 0.12
clpC1 4040902 c.-198T>G upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.17
embB 4248319 c.1806A>T synonymous_variant 0.18
embB 4248324 p.Ala604Gly missense_variant 0.15
aftB 4269693 c.-857C>T upstream_gene_variant 1.0
ethA 4327603 c.-130G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338649 c.-128C>T upstream_gene_variant 0.41
gid 4407670 p.Met178Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0