TB-Profiler result

Run: ERR13246255
Summary

Run ID: ERR13246255

Sample name:

Date: 2025-02-11T16:39:14.981658

Number of reads: 1809704

Percentage reads mapped: 99.17

Median coverage: 91.0

Strain: lineage4.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
lineage4.4.2 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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 7045 c.-257C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
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 8414 c.1113C>T synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8417 c.1116C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8420 c.1119T>C synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 8442 c.1141C>T synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 8453 c.1152A>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8459 c.1158G>A synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 8462 c.1161A>G synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 8465 c.1164C>G synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 8471 c.1170T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8480 c.1179C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8486 c.1185T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8489 c.1188A>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8501 c.1200G>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156588 c.-479_-478delGT upstream_gene_variant 1.0 isoniazid Uncertain significance
PPE35 2169820 p.Asn265Asp missense_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747461 c.138C>T synonymous_variant 0.99 para-aminosalicylic_acid
Rv2477c 2783332 c.711T>C synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783344 c.699C>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783350 c.693T>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783353 c.690T>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783359 c.684G>A synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783386 c.657G>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783395 c.648T>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783422 c.621T>G synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783425 c.618C>G synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783432 p.Ser204Ala missense_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783440 c.603T>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783461 c.582T>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783464 c.579A>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783467 c.576G>C synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783473 c.570A>C synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783499 c.544T>C synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783502 c.541T>C synonymous_variant 0.12 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783512 c.531A>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783520 c.523T>C synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2477c 2783527 c.516A>G synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3066099 p.Met31Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624817 p.Glu32Lys missense_variant 1.0 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878217 c.291A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878262 p.Ser82Gly missense_variant 0.13 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.14 rifampicin Uncertain significance
rpoA 3878295 c.213A>G synonymous_variant 0.14 rifampicin
rpoA 3878322 c.186A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.13 rifampicin
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326066 p.Arg470Cys missense_variant 1.0 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 1.0 kanamycin
capreomycin
amikacin