TB-Profiler result

Run: ERR13266817
Summary

Run ID: ERR13266817

Sample name:

Date: 2025-02-11T09:28:07.461646

Number of reads: 4695741

Percentage reads mapped: 99.64

Median coverage: 127.0

Strain: 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 0.99
lineage3.1 East-African-Indian RD750 0.58
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Leu 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.Met306Val Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
gyrA 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
gyrB 6742 p.Glu501Asp missense_variant 0.51 levofloxacin Assoc w R - Interim
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 0.5 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761101 p.Gln432Leu missense_variant 0.67 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.43 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 0.5 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.47 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.55 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.54 streptomycin 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 8405 p.His368Gln missense_variant 0.46 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9788 c.2487C>T synonymous_variant 0.6 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.99 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
rpoB 759608 c.-199C>T upstream_gene_variant 0.5 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.97 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764822 p.Asp485Tyr missense_variant 0.58 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775675 p.Trp936Arg missense_variant 0.46 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303428 c.498C>A synonymous_variant 0.57 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304265 c.1335C>T synonymous_variant 0.53 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1305215 p.Ser762Asn missense_variant 0.43 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474222 n.565G>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid
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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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 0.98 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.99 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99 isoniazid Not assoc w R
folC 2746268 p.Thr444Ile missense_variant 0.46 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.98 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
pepQ 2859624 c.795G>A synonymous_variant 0.36 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv2681 2996975 c.237G>A synonymous_variant 0.4 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640671 c.129T>C synonymous_variant 0.46 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiB 3642005 c.471C>G synonymous_variant 0.5 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoA 3878590 c.-84delC upstream_gene_variant 0.51 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.99 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.99 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 4139067 p.Glu230Ala missense_variant 0.42 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4241033 p.Pro391Ser missense_variant 0.51 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326912 p.Val188Ile missense_variant 0.65 ethionamide Uncertain significance
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 4407955 p.Arg83Leu missense_variant 0.44 streptomycin Uncertain significance