TB-Profiler result

Run: SRR19428585
Summary

Run ID: SRR19428585

Sample name:

Date: 2024-10-04T16:55:25.480115

Number of reads: 1828128

Percentage reads mapped: 99.59

Median coverage: 87.0

Strain: lineage1.1.2;lineage3.1.1;lineage4.3;lineage4.6.1.1

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 0.68
lineage1.1.2 Indo-Oceanic RD239 0.06
lineage4.3 Euro-American (LAM) None 0.06
lineage4.6 Euro-American None 0.1
lineage3.1.1 East-African-Indian RD750 0.41
lineage1.1 Indo-Oceanic RD239 0.12
lineage4 Euro-American None 0.14
lineage4.6.1.1 Euro-American RD724 0.09
lineage1 Indo-Oceanic RD239 0.07
lineage3.1 East-African-Indian RD750 0.37
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
dnaA 1277 p.Thr426Ile missense_variant 0.29 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 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 13250 c.309G>A synonymous_variant 0.2 isoniazid Not assoc w R - Interim
Rv0010c 13298 p.Ile87Met missense_variant 0.11 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.7 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574900 c.-448G>C upstream_gene_variant 0.44 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.12 ethionamide
rpoB 759746 c.-61C>T upstream_gene_variant 0.42 rifampicin Not assoc w R
rpoB 760948 p.Asn381Ser missense_variant 0.12 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.65 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.12 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 1254562 c.-28T>C upstream_gene_variant 0.83 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 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.15 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917777 c.-163A>G upstream_gene_variant 0.12 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.72 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.11 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.84 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.17 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.33 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
pncA 2289047 c.195C>T synonymous_variant 0.44 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.7 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.16 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.7 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.76 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
Rv2681 2997736 c.1009_1011delCCG conservative_inframe_deletion 0.19 capreomycin Uncertain significance
Rv2752c 3064632 c.1560C>T synonymous_variant 0.15 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
thyA 3073868 p.Thr202Ala missense_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.1 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612870 p.Ala83Ser missense_variant 0.28 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.11 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.86 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642098 c.564G>A synonymous_variant 0.44 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840636 p.Pro262Gln missense_variant 0.2 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.17 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.42 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.48 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 4139670 p.Cys29Tyr missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240172 p.Val104Met missense_variant 0.11 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.29 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.52 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.12 ethambutol Not assoc w R
embA 4245883 p.Gly884Asp missense_variant 0.3 ethambutol Uncertain significance
ubiA 4269606 c.228T>C synonymous_variant 0.12 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 0.15 ethionamide
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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.11 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.79 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.11 streptomycin Not assoc w R