TB-Profiler result

Run: SRR25827413
Summary

Run ID: SRR25827413

Sample name:

Date: 2024-10-03T19:16:24.212608

Number of reads: 7073249

Percentage reads mapped: 99.29

Median coverage: 242.0

Strain: lineage2.2.1;lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 0.83
lineage2 East-Asian RD105 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.18
lineage2.2 East-Asian (Beijing) RD105;RD207 0.17
lineage4 Euro-American None 0.81
lineage4.3.3 Euro-American (LAM) RD115 0.8
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin
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
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 0.15 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.18 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.12 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 8040 p.Gly247Ser missense_variant 0.8 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 491742 c.960T>C synonymous_variant 0.21 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.17 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.16 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.18 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.19 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.17 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.19 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.84 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 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.2 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18 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 0.21 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 0.15 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.86 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 0.19 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.2 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
kasA 2518919 p.Gly269Ser missense_variant 0.8 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.78 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.84 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.15 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.17 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 0.16 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640211 c.-332T>G upstream_gene_variant 0.13 pretomanid
delamanid
clofazimine
clpC1 4038287 c.2418C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.19 ethambutol Not assoc w R
embA 4243798 p.Val189Ala missense_variant 0.81 ethambutol
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.2 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.21 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 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.21 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.83 streptomycin Not assoc w R