TB-Profiler result

Run: SRR19415520
Summary

Run ID: SRR19415520

Sample name:

Date: 2024-10-05T03:41:49.677677

Number of reads: 817402

Percentage reads mapped: 99.53

Median coverage: 34.0

Strain: lineage1.1.2;lineage3.1.1;lineage4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.82
lineage1.1.2 Indo-Oceanic RD239 0.07
lineage3.1.1 East-African-Indian RD750 0.11
lineage1.1 Indo-Oceanic RD239 0.08
lineage4 Euro-American None 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
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
gyrB 6140 p.Val301Leu missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9143 c.1842T>C synonymous_variant 0.14 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 13460 c.99T>C synonymous_variant 0.27 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.97 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574900 c.-448G>C upstream_gene_variant 0.5 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.76 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.21 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.67 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.96 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 0.9 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253330 p.Gly402Glu missense_variant 0.48 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254253 c.282C>T synonymous_variant 0.74 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
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 0.87 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.23 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.84 pyrazinamide Not assoc w R
Rv1979c 2221783 p.Ala461Glu missense_variant 0.15 bedaquiline Uncertain significance
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.17 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.82 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.85 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.82 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2680 2996025 c.-79_-76delAGAG upstream_gene_variant 0.62 capreomycin
Rv2752c 3064632 c.1560C>T synonymous_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 0.21 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3626907 p.Asn148Ser missense_variant 0.59 rifampicin Uncertain significance
bedaquiline
fbiA 3640210 c.-333C>G upstream_gene_variant 0.47 pretomanid
delamanid
clofazimine
fbiB 3642098 c.564G>A synonymous_variant 0.58 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840636 p.Pro262Gln missense_variant 0.58 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.23 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.29 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138791 p.Ser322Trp missense_variant 0.16 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4241562 p.Arg567His missense_variant 0.28 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.9 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243813 p.Arg194Gln missense_variant 0.22 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.28 ethambutol Not assoc w R
embA 4245883 p.Gly884Asp missense_variant 0.55 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.19 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.36 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 4338603 c.-82C>T upstream_gene_variant 0.24 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 0.81 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.28 streptomycin Not assoc w R