TB-Profiler result

Run: SRR1173725
Summary

Run ID: SRR1173725

Sample name:

Date: 2024-10-05T12:58:22.735860

Number of reads: 1926526

Percentage reads mapped: 93.57

Median coverage: 19.0

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 0.99
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
p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Leu85Arg Assoc w R
p.Pro54Gln Assoc w R - Interim
streptomycin gid c.442_443insC 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
rpoB 761127 p.Ser441Ala missense_variant 0.5 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
inhA 1674481 p.Ser94Ala missense_variant 1.0 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288988 p.Leu85Arg missense_variant 0.19 pyrazinamide Assoc w R
pncA 2289081 p.Pro54Gln missense_variant 0.78 pyrazinamide Assoc w R - Interim
gid 4407760 c.442_443insC 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 8553 p.Arg418Trp missense_variant 1.0 levofloxacin
moxifloxacin
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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574788 c.-560C>G upstream_gene_variant 0.48 isoniazid
ethionamide
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
mmpL5 775611 p.Ser957* stop_gained 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
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 779536 c.-631G>A upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253355 p.Val394Met missense_variant 0.97 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1253690 p.Ala282Gly missense_variant 0.31 levofloxacin
moxifloxacin
isoniazid
rifampicin
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 1302667 c.-264G>A upstream_gene_variant 0.94 pretomanid
delamanid
clofazimine
Rv1258c 1406466 p.Ser292Leu missense_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417464 c.-117C>T upstream_gene_variant 1.0 ethambutol
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471628 n.-218C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155155 c.957C>T synonymous_variant 1.0 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168701 p.Val638Ile missense_variant 1.0 pyrazinamide
PPE35 2168924 c.1689G>T synonymous_variant 0.99 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 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
kasA 2518132 c.18C>T synonymous_variant 0.92 isoniazid
eis 2714418 c.915C>T synonymous_variant 1.0 kanamycin
amikacin
ahpC 2726247 p.Ile19Val missense_variant 0.29 isoniazid
Rv2477c 2784139 c.-98delC upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
pepQ 2859482 p.Ala313Thr missense_variant 1.0 bedaquiline
clofazimine
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 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625413 p.Ala401Ser missense_variant 1.0 rifampicin
bedaquiline
mtrB 3626025 c.589C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline 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 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
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 4247252 p.Ser247Ala missense_variant 1.0 ethambutol
embB 4247483 p.Gly324Arg missense_variant 0.58 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
aftB 4267683 p.Trp385Ser missense_variant 0.18 ethambutol
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R