TB-Profiler result

Run: SRR29539801
Summary

Run ID: SRR29539801

Sample name:

Date: 2024-10-04T03:16:26.914995

Number of reads: 2751451

Percentage reads mapped: 99.57

Median coverage: 77.0

Strain: lineage2.2.1;lineage4.2.1

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.15
lineage4.2 Euro-American None 0.85
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.13
lineage2.2 East-Asian (Beijing) RD105;RD207 0.14
lineage4 Euro-American None 0.84
lineage4.2.1 Euro-American (TUR) None 0.84
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.18 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.1 isoniazid Assoc w R High-level resistance
embA 4243221 c.-12C>T upstream_gene_variant 0.12 ethambutol Uncertain significance Mutation from literature
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
gyrA 9337 p.Gln679Arg missense_variant 0.1 levofloxacin
moxifloxacin
fgd1 491742 c.960T>C synonymous_variant 0.18 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.13 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.13 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.22 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.24 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 0.18 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.17 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.86 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.17 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
bacA 2063685 c.1044G>A synonymous_variant 0.92 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.83 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.83 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3065832 c.360C>T synonymous_variant 0.9 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086731 c.-89A>G upstream_gene_variant 0.14 cycloserine
ald 3086742 c.-78A>C upstream_gene_variant 0.85 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
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
alr 3841612 c.-193_-192insC upstream_gene_variant 0.78 cycloserine
panD 4044424 c.-143A>G upstream_gene_variant 0.83 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.12 ethambutol Not assoc w R - Interim
embB 4248212 p.Ala567Thr missense_variant 0.81 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 0.95 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.18 ethambutol Not assoc w R
ethA 4327779 c.-306G>A upstream_gene_variant 0.81 ethionamide
ethA 4328376 c.-903G>C upstream_gene_variant 0.89 ethionamide
whiB6 4338371 p.Thr51Pro missense_variant 0.13 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin 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 0.16 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.12 streptomycin Not assoc w R