TB-Profiler result

Run: SRR29231780
Summary

Run ID: SRR29231780

Sample name:

Date: 2025-02-11T14:49:28.687176

Number of reads: 4026567

Percentage reads mapped: 99.6

Median coverage: 116.0

Strain: lineage4.3.3;lineage4.3.4.2;lineage4.6.1.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.71
lineage4.6 Euro-American None 0.24
lineage4 Euro-American None 1.0
lineage4.6.1.1 Euro-American RD724 0.21
lineage4.3.3 Euro-American (LAM) RD115 0.63
lineage4.6.1 Euro-American (Uganda) RD724 0.24
lineage4.3.4 Euro-American (LAM) RD174 0.08
lineage4.3.4.2 Euro-American (LAM) RD174 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu19Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.14 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.1 streptomycin Assoc w R
pncA 2289186 p.Leu19Pro missense_variant 0.15 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.15 ethambutol Assoc w R
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 Drugs Confidence
gyrB 5723 p.Ala162Ser missense_variant 0.63 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575240 c.-108G>A upstream_gene_variant 0.63 isoniazid Uncertain significance
ethionamide Uncertain significance
hadA 732265 c.336G>A synonymous_variant 0.17 isoniazid Not assoc w R - Interim
rpoC 764840 p.Ile491Val missense_variant 0.12 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.77 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253754 p.Thr261Pro missense_variant 0.22 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155566 c.546G>T synonymous_variant 0.6 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.63 isoniazid
Rv2477c 2783992 c.51T>C synonymous_variant 0.63 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2681 2996876 c.138A>C synonymous_variant 0.25 capreomycin Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.75 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.74 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.17 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
lpqB 3624728 c.183C>T synonymous_variant 0.27 rifampicin
bedaquiline
lpqB 3624748 p.Phe55Leu missense_variant 0.65 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.69 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.76 pyrazinamide Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.68 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 0.2 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.97 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.72 streptomycin Not assoc w R