TB-Profiler result

Run: SRR25827296
Summary

Run ID: SRR25827296

Sample name:

Date: 2024-10-03T23:05:34.538887

Number of reads: 6816754

Percentage reads mapped: 99.23

Median coverage: 235.0

Strain: lineage2.2.1;lineage4.3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.43
lineage2 East-Asian RD105 0.54
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.56
lineage2.2 East-Asian (Beijing) RD105;RD207 0.58
lineage4 Euro-American None 0.43
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val 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 embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
c.187_188insT 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
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
gyrA 7570 p.Ala90Val missense_variant 0.4 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.57 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761110 p.Asp435Val missense_variant 0.38 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.6 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.5 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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 2288847 p.Gly132Ala missense_variant 0.56 pyrazinamide Assoc w R
pncA 2289054 c.187_188insT frameshift_variant 0.45 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.51 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.56 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
Rv0010c 13835 c.-277C>T upstream_gene_variant 0.4 isoniazid
fgd1 491290 p.Val170Met missense_variant 0.54 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.58 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.58 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.59 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.53 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.56 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.47 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 0.63 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.59 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.51 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 0.6 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 0.58 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472920 n.1077dupT non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.67 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 0.55 isoniazid Not assoc w R
katG 2155168 p.Ser315Ala missense_variant 0.6 isoniazid
katG 2156704 c.-593C>T upstream_gene_variant 0.4 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.57 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
folC 2746932 p.Ala223Thr missense_variant 0.42 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.42 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65 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 0.58 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.5 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.55 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.59 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 0.5 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.5 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.54 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.46 streptomycin Not assoc w R