TB-Profiler result

Run: SRR25827371
Summary

Run ID: SRR25827371

Sample name:

Date: 2024-04-16T11:46:07.635770

Number of reads: 9307229

Percentage reads mapped: 99.22

Median coverage: 320.0

Strain: lineage2.2.1;lineage4.8

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
lineage2 East-Asian RD105 0.57
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.54
lineage2.2 East-Asian (Beijing) RD105;RD207 0.57
lineage4 Euro-American None 0.44
lineage4.8 Euro-American (mainly T) RD219 0.44
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
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.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala 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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>C Uncertain significance Mutation from literature
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
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 0.57 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)
rpoB 761155 p.Ser450Leu missense_variant 0.62 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.55 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.51 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.53 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.53 pyrazinamide Assoc w R
eis 2715342 c.-10G>C upstream_gene_variant 0.6 kanamycin Uncertain significance Mutation from literature
thyX 3067961 c.-16C>T upstream_gene_variant 0.6 para-aminosalicylic_acid Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.6 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 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.65 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.55 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.59 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.59 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.36 ethionamide Uncertain significance
Rv0565c 656528 p.Glu315Lys missense_variant 0.39 ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.61 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.43 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.56 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.58 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 0.6 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.61 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.52 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 0.53 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 0.53 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.52 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.62 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 0.53 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.59 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.4 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
Rv2477c 2784204 c.-162A>C upstream_gene_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.46 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.58 cycloserine
whiB7 3569241 c.-562C>G upstream_gene_variant 0.38 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.55 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.49 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.58 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.55 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.43 pyrazinamide Not assoc w R
panD 4045121 c.-840C>T upstream_gene_variant 0.35 pyrazinamide
embC 4241022 p.Ala387Val missense_variant 0.57 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.54 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.18 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.6 ethambutol Not assoc w R
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 0.58 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.59 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.61 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.54 streptomycin Not assoc w R