TB-Profiler result

Run: ERR12115321
Summary

Run ID: ERR12115321

Sample name:

Date: 2024-04-16T04:12:50.075020

Number of reads: 9955744

Percentage reads mapped: 99.64

Median coverage: 270.0

Strain: lineage8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage8 Lineage 8 None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
isoniazid inhA p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin gid c.286delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin Assoc w R
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim
gid 4407916 c.286delC frameshift_variant 1.0 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 9143 c.1842T>C synonymous_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 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 732330 p.Leu134Pro missense_variant 1.0 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765772 c.2403C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 775611 p.Ser957* stop_gained 1.0 clofazimine Uncertain significance
bedaquiline 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779536 c.-631G>A upstream_gene_variant 1.0 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 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302667 c.-264G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
sigE 1365061 p.Thr217Ala missense_variant 1.0 pyrazinamide
Rv1258c 1406466 p.Ser292Leu missense_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417464 c.-117C>T upstream_gene_variant 1.0 ethambutol
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417873 c.-526G>T upstream_gene_variant 1.0 ethambutol
rrs 1471628 n.-218C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853922 p.Ser106* stop_gained 1.0 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917642 c.-298C>T upstream_gene_variant 1.0 capreomycin
tlyA 1917786 c.-154G>A upstream_gene_variant 1.0 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155155 c.957C>T synonymous_variant 1.0 isoniazid
katG 2155172 p.Thr314Ala missense_variant 1.0 isoniazid
katG 2155430 p.Ile228Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168701 p.Val638Ile missense_variant 1.0 pyrazinamide
PPE35 2168711 c.1902A>G synonymous_variant 1.0 pyrazinamide
PPE35 2168924 c.1689G>T synonymous_variant 1.0 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
eis 2714418 c.915C>T synonymous_variant 1.0 amikacin
kanamycin
Rv2477c 2784139 c.-98delC upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
pepQ 2859482 p.Ala313Thr missense_variant 1.0 clofazimine
bedaquiline
Rv2681 2997635 p.Phe299Leu missense_variant 1.0 capreomycin
thyA 3074400 c.72C>G synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3074591 c.-120T>G upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449865 c.1362G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612540 p.Leu193Phe missense_variant 1.0 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625413 p.Ala401Ser missense_variant 1.0 bedaquiline
rifampicin
mtrB 3626025 c.589C>T synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
alr 3840800 c.621C>A synonymous_variant 1.0 cycloserine
clpC1 4039645 p.His354Asp missense_variant 1.0 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246799 p.Gly96Arg missense_variant 1.0 ethambutol
embB 4247252 p.Ser247Ala missense_variant 1.0 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248022 p.Leu503Phe missense_variant 1.0 ethambutol
embB 4248206 p.Ser565Gly missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326264 p.Arg404Cys missense_variant 1.0 ethionamide
ethA 4326682 p.Phe264Leu missense_variant 1.0 ethionamide Uncertain significance
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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R