TB-Profiler result

Run: ERR13266555

Summary

Run ID: ERR13266555

Sample name:

Date: 2025-02-11T18:20:44.114436

Number of reads: 2447049

Percentage reads mapped: 98.12

Median coverage: 69.0

Strain: lineage2.2.1

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
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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.Asp94Gly missense_variant 0.94 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.93 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.95 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.91 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.94 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.98 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.98 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763528 c.159G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764005 c.636G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764011 c.642T>C synonymous_variant 0.14 rifampicin
rpoC 764024 c.655T>C synonymous_variant 0.16 rifampicin
rpoC 764040 p.Ser224Thr missense_variant 0.15 rifampicin
rpoC 764044 c.675T>G synonymous_variant 0.14 rifampicin
rpoC 764059 c.690G>T synonymous_variant 0.15 rifampicin
rpoC 764840 p.Ile491Val missense_variant 0.84 rifampicin Uncertain significance
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674820 c.619_621delCTCinsTTG synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674828 c.627G>A synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674846 p.Ile215Met missense_variant 0.14 isoniazid
ethionamide
inhA 1674870 c.669T>C synonymous_variant 0.12 isoniazid
ethionamide
rpsA 1833595 c.54T>C synonymous_variant 0.12 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833703 c.162C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1833724 c.183C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1833790 c.249T>C synonymous_variant 0.12 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833808 c.267G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.2 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.18 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.16 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833895 c.354G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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 2154724 p.Arg463Leu missense_variant 0.97 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.98 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
Rv2477c 2782669 p.Lys458Asn missense_variant 0.97 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626876 c.-263A>G upstream_gene_variant 0.12 rifampicin
bedaquiline
rpoA 3877613 p.Ile299Val missense_variant 0.11 rifampicin
rpoA 3878022 c.486T>C synonymous_variant 0.12 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.12 rifampicin
rpoA 3878346 c.162T>C synonymous_variant 0.14 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.14 rifampicin
rpoA 3878370 c.138T>C synonymous_variant 0.15 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.15 rifampicin
rpoA 3878384 c.124C>T synonymous_variant 0.13 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.13 rifampicin
rpoA 3878391 c.117T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
embC 4241022 p.Ala387Val missense_variant 0.99 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.98 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.96 ethambutol Not assoc w R
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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.98 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R