TB-Profiler result

Run: SRR10040438
Summary

Run ID: SRR10040438

Sample name:

Date: 2024-04-16T05:27:09.591156

Number of reads: 4476960

Percentage reads mapped: 99.17

Median coverage: 122.0

Strain: lineage2.2.1;lineage4.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.8
lineage2 East-Asian RD105 0.19
lineage4.2 Euro-American None 0.82
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.16
lineage2.2 East-Asian (Beijing) RD105;RD207 0.15
lineage4 Euro-American None 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.His445Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Arg 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
rpoB 761139 p.His445Tyr missense_variant 0.25 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.15 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
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 491742 c.960T>C synonymous_variant 0.12 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.79 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.15 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.17 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.16 ethionamide Uncertain significance
rpoB 761237 p.Met477Ile missense_variant 0.17 rifampicin
rpoB 762715 p.Val970Ala missense_variant 0.81 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.21 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 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777907 c.574C>T synonymous_variant 0.11 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781398 c.-162A>G upstream_gene_variant 0.1 streptomycin Uncertain significance
rplC 800204 c.-605T>C upstream_gene_variant 0.84 linezolid
sigE 1364802 c.390C>T synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.13 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673600 p.Gly54Ala missense_variant 0.13 ethionamide
isoniazid
inhA 1674696 c.495G>A synonymous_variant 0.16 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.2 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 0.94 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.12 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
Rv1979c 2223770 c.-670_-607delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG upstream_gene_variant 0.92 clofazimine
bedaquiline
Rv1979c 2223770 c.-669_-607delTGGAAAATTACATCGCCCAGACGCGCGACAAGTTCCTCAGCGCGGCCACATCGTCCACTCCAC upstream_gene_variant 0.75 clofazimine
bedaquiline
pncA 2289998 c.-757C>T upstream_gene_variant 0.9 pyrazinamide
Rv2752c 3066276 c.-85G>A upstream_gene_variant 0.82 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.82 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.75 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612469 c.648A>G synonymous_variant 0.8 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18 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 0.29 bedaquiline Uncertain significance
rifampicin 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 0.18 ethambutol Not assoc w R
embA 4244100 p.Val290Ile missense_variant 0.14 ethambutol
ethA 4326676 p.Ser266Arg missense_variant 0.11 ethionamide Uncertain significance
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 0.28 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.13 streptomycin Not assoc w R
gid 4407940 p.Val88Ala missense_variant 0.88 streptomycin Uncertain significance