TB-Profiler result

Run: SRR25827513
Summary

Run ID: SRR25827513

Sample name:

Date: 2024-04-16T04:15:42.489096

Number of reads: 9708260

Percentage reads mapped: 98.49

Median coverage: 319.0

Strain: lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.26
lineage2 East-Asian RD105 0.73
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.72
lineage2.2 East-Asian (Beijing) RD105;RD207 0.72
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
p.Ile480Val Uncertain significance Mutation from literature
p.Ile491Phe Assoc w R
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
p.Thr275Ala Uncertain significance Mutation from literature
ethambutol embA c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
p.Met1? Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
n.906A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrB p.Arg446Cys Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Arg446Cys Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.144dupC 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
gyrB 6575 p.Arg446Cys missense_variant 0.34 moxifloxacin Uncertain significance Mutation from literature
levofloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Gly missense_variant 0.67 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin Assoc w R
rpoB 761244 p.Ile480Val missense_variant 0.35 rifampicin Uncertain significance Mutation from literature
rpoB 761277 p.Ile491Phe missense_variant 0.38 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.35 clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.41 streptomycin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 0.19 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 1.0 isoniazid Assoc w R High-level resistance
katG 2155289 p.Thr275Ala missense_variant 0.22 isoniazid Uncertain significance Mutation from literature
pncA 2289162 p.Leu27Pro missense_variant 0.19 pyrazinamide Assoc w R
pncA 2289240 p.Met1? start_lost 0.38 pyrazinamide Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 0.18 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.67 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.3 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 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 0.51 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.72 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 0.75 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.27 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.32 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.28 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.17 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 0.56 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.73 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 0.7 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416622 c.726C>T synonymous_variant 0.18 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.73 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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
pncA 2289047 c.195C>T synonymous_variant 0.33 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.24 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.25 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ribD 2987506 p.Leu223Arg missense_variant 0.16 para-aminosalicylic_acid
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.31 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067949 c.-4C>T upstream_gene_variant 0.15 para-aminosalicylic_acid
thyA 3073687 p.Ala262Val missense_variant 0.27 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449326 p.Arg275Ser missense_variant 0.36 ethionamide
whiB7 3568555 p.Leu42Pro missense_variant 0.21 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.16 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
lpqB 3623174 c.1737G>C synonymous_variant 0.24 bedaquiline Not assoc w R - Interim
rifampicin 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 0.65 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.3 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.23 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.29 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.24 ethambutol 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 0.76 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.19 ethambutol
embB 4247015 p.Ser168Ala missense_variant 0.28 ethambutol
aftB 4267492 p.Ala449Thr missense_variant 0.25 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.63 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.18 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 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.75 streptomycin Not assoc w R
gid 4408114 p.Gly30Asp missense_variant 0.29 streptomycin Uncertain significance