TB-Profiler result

Run: SRR22175193
Summary

Run ID: SRR22175193

Sample name:

Date: 2024-04-16T06:02:59.658316

Number of reads: 7310695

Percentage reads mapped: 99.32

Median coverage: 220.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
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.Ile491Thr 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)
c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. 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 embA c.-16C>T Uncertain significance Mutation from literature
c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine alr p.Met343Thr Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
delamanid
bedaquiline mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
gyrA 7570 p.Ala90Val missense_variant 1.0 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7582 p.Asp94Gly missense_variant 0.31 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.4 rifampicin Uncertain significance Mutation from literature
mmpR5 779181 c.198dupG frameshift_variant 0.34 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.64 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)
inhA 1673432 c.-770T>A upstream_gene_variant 0.36 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.61 pyrazinamide Assoc w R
pncA 2289228 p.Ile5Ser missense_variant 0.34 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.41 kanamycin Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.4 para-aminosalicylic_acid Mutation from literature
alr 3840393 p.Met343Thr missense_variant 0.45 cycloserine Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol Uncertain significance Mutation from literature
embA 4243222 c.-11C>A upstream_gene_variant 0.55 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.65 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
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 491290 p.Val170Met missense_variant 0.39 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.37 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.74 rifampicin Uncertain significance
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.29 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 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 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 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 1.0 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
thyX 3067949 c.-4C>T upstream_gene_variant 0.34 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568435 c.242_245delGTCCinsATCCTT frameshift_variant&missense_variant 0.36 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3568442 p.Lys80Gln missense_variant 0.35 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3568443 p.His79Gln missense_variant 0.35 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3568854 c.-176delG upstream_gene_variant 0.7 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.66 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99 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 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.34 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247847 p.Gln445Arg missense_variant 0.38 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.99 ethambutol Not assoc w R
ethA 4326513 p.Thr321Pro missense_variant 0.66 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.55 ethionamide Uncertain significance
ethA 4327344 p.Thr44Pro missense_variant 0.37 ethionamide Uncertain significance
whiB6 4338292 p.Ala77Val missense_variant 0.42 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.43 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R