TB-Profiler result

Run: ERR7737753
Summary

Run ID: ERR7737753

Sample name:

Date: 2024-10-05T00:42:18.395680

Number of reads: 1497189

Percentage reads mapped: 99.4

Median coverage: 44.0

Strain: lineage7

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage7 Lineage 7 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.Ser450Leu 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.Gln127Pro Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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 2155732 p.Gln127Pro missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol 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 8876 c.1575C>T synonymous_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 13330 p.Gln77* stop_gained 1.0 isoniazid Uncertain significance
Rv0010c 13445 c.114G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv0010c 13563 c.-5A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656656 p.Ala272Val missense_variant 1.0 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
mmaA3 737363 p.Glu263* stop_gained 1.0 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764013 p.Glu215Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 766955 p.Glu1196Lys missense_variant 1.0 rifampicin 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
mmpL5 776202 p.Gly760Ala missense_variant 1.0 bedaquiline
clofazimine
mmpL5 778024 p.Leu153Val missense_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781488 c.-72G>A upstream_gene_variant 1.0 streptomycin
rplC 800307 c.-502_-501insCGCGACAAGGC upstream_gene_variant 1.0 linezolid
Rv1129c 1253707 c.828A>C synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
Rv1129c 1254136 p.Glu133Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254519 p.Val6Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin 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
fbiC 1304031 c.1101C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1305129 c.2199C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
embR 1416977 p.His124Arg missense_variant 1.0 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474959 n.1303_1304insAC non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rpsA 1834916 p.Thr459Pro missense_variant 1.0 pyrazinamide
tsnR 1853849 c.245dupC frameshift_variant 1.0 linezolid Uncertain significance
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
tlyA 1918281 c.342A>C synonymous_variant 1.0 capreomycin
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064234 p.Trp165* stop_gained 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
ndh 2102218 c.825C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
delamanid
ethionamide
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 2169232 p.Thr461Ala missense_variant 1.0 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 1.0 isoniazid
ahpC 2726121 c.-72C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2681 2997746 c.1008G>A synonymous_variant 1.0 capreomycin
Rv2681 2998027 p.Ala430Val missense_variant 1.0 capreomycin
Rv2752c 3065880 c.312C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448540 p.Gly13Ser missense_variant 1.0 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878040 c.468T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
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
glpK 4139014 p.Pro248Ser missense_variant 0.26 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240153 c.291G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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 4245701 c.-813G>A upstream_gene_variant 1.0 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248073 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4267649 c.1188T>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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 4327065 p.Cys137Arg missense_variant 1.0 ethionamide Uncertain significance
ethA 4328371 c.-898C>T upstream_gene_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
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 4407991 p.Gly71Val missense_variant 1.0 streptomycin