TB-Profiler result

Run: ERR15686468
Summary

Run ID: ERR15686468

Sample name:

Date: 2025-12-15T11:15:37.132567

Number of reads: 8064946

Percentage reads mapped: 99.51

Median coverage: 234.0

Strain: lineage4.5

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 Euro-American None 100.0
lineage4.5 Euro-American RD122 100.0
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 ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.391dupG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala 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 7582 p.Asp94Ala missense_variant 1.0 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
pncA 2288850 c.391dupG frameshift_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 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
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 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8207 c.906T>C synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 amikacin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
nusG 734735 p.Ala161Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 765863 p.Ile832Val missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779029 p.Pro14Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253247 p.Thr430Pro missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0 isoniazid Not assoc w R
pyrazinamide Not assoc w R - Interim
streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1475952 n.2295A>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834252 c.711C>A synonymous_variant 1.0 pyrazinamide Uncertain significance
tsnR 1853597 c.-9G>C upstream_gene_variant 1.0 linezolid Uncertain significance
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
katG 2155552 p.Arg187Gln missense_variant 1.0 isoniazid Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 1.0 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
Rv2752c 3065626 p.Ser189* stop_gained 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
whiB7 3568649 p.Pro11Ser missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627533 c.-184G>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
ddn 3987299 c.456A>C stop_lost&splice_region_variant 0.12 delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038328 p.Glu793Lys missense_variant 0.99 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243532 c.300C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338365 p.Cys53Gly missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407949 p.Asp85Ala missense_variant 1.0 streptomycin Uncertain significance