TB-Profiler result

Run: SRR25827733
Summary

Run ID: SRR25827733

Sample name:

Date: 2025-02-11T18:52:17.859114

Number of reads: 9156779

Percentage reads mapped: 99.08

Median coverage: 290.0

Strain: lineage3;lineage4.2.2.2

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.31
lineage3 East-African-Indian RD750 0.65
lineage4.2 Euro-American None 0.32
lineage4 Euro-American None 0.33
lineage4.2.2.2 Euro-American (Ural) None 0.32
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Phe Assoc w R
p.Ser450Leu Assoc w R
p.Ile480Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.238delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ser91Pro Assoc w R
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
gyrA 7572 p.Ser91Pro missense_variant 0.34 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761109 p.Asp435Phe missense_variant 0.62 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.36 rifampicin Assoc w R
rpoB 761244 p.Ile480Val missense_variant 0.35 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.58 ethambutol Assoc w R
gid 4407964 c.238delG frameshift_variant 0.68 streptomycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13321 p.Arg80* stop_gained 0.34 isoniazid Uncertain significance
Rv0010c 13649 c.-91G>A upstream_gene_variant 0.65 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.66 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575537 p.Asp64Asn missense_variant 0.67 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 576077 c.730C>T synonymous_variant 0.29 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
mshA 576453 p.Val369Gly missense_variant 0.23 isoniazid
ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 0.7 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.33 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.72 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.72 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.67 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.6 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
rplC 800204 c.-605T>C upstream_gene_variant 0.29 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302927 c.-4C>T upstream_gene_variant 0.33 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.32 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.37 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.68 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288772 p.Val157Gly missense_variant 0.3 pyrazinamide Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.64 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.63 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.65 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.65 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
pepQ 2860183 p.Val79Gly missense_variant 0.19 bedaquiline
clofazimine
ribD 2986827 c.-12G>A upstream_gene_variant 0.35 para-aminosalicylic_acid
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.36 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.33 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.64 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240327 c.465G>A synonymous_variant 0.35 ethambutol Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.65 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43G>C upstream_gene_variant 0.32 ethambutol Uncertain significance
embA 4244608 p.Leu459Arg missense_variant 0.72 ethambutol Uncertain significance
embB 4246710 p.Ser66Thr missense_variant 0.62 ethambutol
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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.68 streptomycin Not assoc w R