TB-Profiler result

Run: SRR15600373
Summary

Run ID: SRR15600373

Sample name:

Date: 2024-10-04T04:11:16.131023

Number of reads: 5576373

Percentage reads mapped: 99.65

Median coverage: 178.0

Strain: lineage2.2.1.1;lineage4.8

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 0.83
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.81
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage4 Euro-American None 0.22
lineage4.8 Euro-American (mainly T) RD219 0.19
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 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 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)
ethambutol
pyrazinamide pncA c.-11A>C Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 0.15 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.83 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.2 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)
pncA 2289252 c.-11A>C upstream_gene_variant 0.84 pyrazinamide 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
dnaA 1139 p.Thr380Ile missense_variant 0.11 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.79 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.8 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.21 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.23 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.9 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.21 rifampicin Not assoc w R
rpoB 761253 p.Pro483Ser missense_variant 0.15 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 764670 p.Pro434Leu missense_variant 0.13 rifampicin Uncertain significance
rpoC 765113 p.Val582Met missense_variant 0.16 rifampicin Uncertain significance
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 0.82 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.84 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.8 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 0.84 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 0.83 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.76 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.81 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154250 p.Ala621Val missense_variant 0.15 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.83 isoniazid Not assoc w R
katG 2155586 p.Met176Val missense_variant 0.84 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.72 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.17 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
eis 2714846 p.Val163Ile missense_variant 0.8 kanamycin Not assoc w R
amikacin Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.23 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.8 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.15 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.81 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.82 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.17 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.25 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.82 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.77 ethambutol Not assoc w R - Interim
embB 4248115 c.1602C>T synonymous_variant 0.84 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.76 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 0.76 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.8 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.81 streptomycin Not assoc w R