TB-Profiler result

Run: SRR15316381
Summary

Run ID: SRR15316381

Sample name:

Date: 2024-10-05T10:21:44.087797

Number of reads: 9327469

Percentage reads mapped: 99.57

Median coverage: 286.0

Strain: lineage2.2.1;lineage4.4.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.21
lineage2 East-Asian RD105 0.64
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.63
lineage2.2 East-Asian (Beijing) RD105;RD207 0.64
lineage4 Euro-American None 0.36
lineage4.4 Euro-American None 0.18
lineage4.4.2 Euro-American None 0.16
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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 7892 c.591G>A synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7914 c.613C>T synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.6 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.2 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.64 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.68 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.6 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 0.64 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.63 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 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 0.64 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 0.65 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407380 c.-40C>T upstream_gene_variant 0.18 streptomycin Uncertain significance
pyrazinamide
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471820 n.-26T>G upstream_gene_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833410 c.-132G>A upstream_gene_variant 0.15 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.64 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 0.59 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.54 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.2 pyrazinamide Not assoc w R
Rv1979c 2222090 p.Leu359Met missense_variant 0.17 bedaquiline
clofazimine
Rv1979c 2222510 p.Ser219Ala missense_variant 0.16 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3065478 p.Phe238Leu missense_variant 0.32 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066099 p.Met31Ile missense_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.79 cycloserine
fbiD 3339480 p.Gln121His missense_variant 0.17 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.11 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.6 pyrazinamide Not assoc w R - Interim
lpqB 3624850 p.Ser21Gly missense_variant 0.16 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.67 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.17 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.17 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.19 ethambutol Not assoc w R
embC 4240629 p.Gly256Asp missense_variant 0.33 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243458 p.Cys76Gly missense_variant 0.15 ethambutol
embA 4243482 p.Ala84Ser missense_variant 0.17 ethambutol Uncertain significance
embA 4246508 c.3276G>A synonymous_variant 0.14 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.61 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.12 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.14 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 0.63 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R