TB-Profiler result

Run: SRR6832014
Summary

Run ID: SRR6832014

Sample name:

Date: 2024-03-26T17:24:02.717926

Number of reads: 3378510

Percentage reads mapped: 99.62

Median coverage: 71.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: HR-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 0.23
lineage2 East-Asian RD105 0.79
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.74
lineage2.2 East-Asian (Beijing) RD105;RD207 0.74
lineage4 Euro-American None 0.25
lineage4.3.3 Euro-American (LAM) RD115 0.24
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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)
c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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.Tyr319Ser Assoc w R
pyrazinamide
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.27 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.22 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1673432 c.-770T>C upstream_gene_variant 0.77 isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
katG 2155168 p.Ser315Thr missense_variant 0.26 isoniazid Assoc w R High-level resistance
embB 4247469 p.Tyr319Ser missense_variant 0.19 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
dnaA 490 p.Gly164Ser missense_variant 0.86 isoniazid Uncertain significance
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 0.21 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 0.69 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.82 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619694 c.-197C>T upstream_gene_variant 0.78 capreomycin
amikacin
kanamycin
ccsA 620625 p.Ile245Met missense_variant 0.73 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.82 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.71 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.79 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.79 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.65 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.74 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.33 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 0.3 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
sigE 1364706 c.294G>A synonymous_variant 0.81 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.83 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.29 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 0.75 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.37 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.5 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.35 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.39 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 0.15 para-aminosalicylic_acid
Rv2680 2996108 c.6delC frameshift_variant 0.28 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.27 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612318 p.Arg267Ser missense_variant 0.69 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.74 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.75 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.22 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.64 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.71 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.88 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.83 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.13 streptomycin Not assoc w R