TB-Profiler result

Run: SRR6339637
Summary

Run ID: SRR6339637

Sample name:

Date: 2024-10-03T22:52:04.610319

Number of reads: 2926069

Percentage reads mapped: 99.43

Median coverage: 92.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.69
lineage4.1 Euro-American None 0.31
lineage4.1.2 Euro-American None 0.34
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.34
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.68
lineage2.2 East-Asian (Beijing) RD105;RD207 0.67
lineage4 Euro-American None 0.31
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
rpoC p.Gly332Arg Uncertain significance Mutation from literature
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Pro69Leu Assoc w R
streptomycin rpsL p.Lys88Arg 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
ethA p.Val202Gly Assoc w R - Interim
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.33 rifampicin Uncertain significance Mutation from literature
rpsL 781822 p.Lys88Arg missense_variant 0.6 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.68 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid Assoc w R High-level resistance
pncA 2289036 p.Pro69Leu missense_variant 0.67 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.61 ethambutol Assoc w R
ethA 4326869 p.Val202Gly missense_variant 0.57 ethionamide Assoc w R - Interim
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 491591 p.Lys270Met missense_variant 0.32 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.65 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.43 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.57 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.64 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.67 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.31 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.28 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.71 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.28 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 0.73 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.68 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7 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 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.34 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 0.73 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 0.69 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 0.7 isoniazid Not assoc w R
katG 2155715 p.Asn133Asp missense_variant 0.64 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.59 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 2518076 c.-39C>T upstream_gene_variant 0.34 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.64 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 0.69 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.23 rifampicin
bedaquiline
alr 3840391 p.Asp344Asn missense_variant 0.8 cycloserine
embC 4239298 c.-565C>T upstream_gene_variant 0.35 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.46 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.79 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.26 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.58 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.5 ethambutol Not assoc w R
whiB6 4338365 p.Cys53Arg missense_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.7 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.62 streptomycin Not assoc w R