TB-Profiler result

Run: SRR29772605
Summary

Run ID: SRR29772605

Sample name:

Date: 2025-02-11T13:22:22.226884

Number of reads: 4429920

Percentage reads mapped: 99.57

Median coverage: 130.0

Strain: lineage1.1.3.1;lineage3.1

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
lineage3 East-African-Indian RD750 0.63
lineage1.1.3 Indo-Oceanic RD239 0.37
lineage1.1 Indo-Oceanic RD239 0.37
lineage1 Indo-Oceanic RD239 0.33
lineage1.1.3.1 Indo-Oceanic RD239 0.36
lineage3.1 East-African-Indian RD750 0.6
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
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
pyrazinamide
streptomycin rrs n.514A>C 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
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 0.63 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 761139 p.His445Tyr missense_variant 0.61 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.67 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.27 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)
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid Assoc w R High-level resistance
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 6112 p.Met291Ile missense_variant 0.39 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 8452 p.Ala384Val missense_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.33 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 13298 p.Ile87Met missense_variant 0.32 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.31 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.34 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.4 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.68 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.71 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.31 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.39 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.4 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779526 c.-621G>A upstream_gene_variant 0.3 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.27 linezolid Not assoc w R
rplC 800899 p.Ala31Thr missense_variant 0.67 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.31 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.35 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.36 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.31 linezolid Not assoc w R
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
bacA 2062922 p.Ile603Val missense_variant 0.35 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.35 pyrazinamide Uncertain significance
PPE35 2170018 p.Ala199Thr missense_variant 0.7 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.45 bedaquiline Not assoc w R - Interim
clofazimine 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 0.65 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.61 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.35 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.44 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.55 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.63 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
Rv2752c 3064632 c.1560C>T synonymous_variant 0.33 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 3074305 p.Ala56Val missense_variant 0.62 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.32 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.29 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841253 c.168C>T synonymous_variant 0.42 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.32 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.62 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.36 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 0.68 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
embC 4240671 p.Thr270Ile missense_variant 0.36 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.38 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.66 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 0.39 ethambutol Not assoc w R
embA 4245386 c.2154C>T synonymous_variant 0.36 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.32 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.37 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.37 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.4 ethambutol Not assoc w R
whiB6 4338594 c.-73T>G upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
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 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.39 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.48 streptomycin Not assoc w R