TB-Profiler result

Run: ERR4797182
Summary

Run ID: ERR4797182

Sample name:

Date: 2024-04-16T04:52:44.058559

Number of reads: 3228677

Percentage reads mapped: 99.3

Median coverage: 96.0

Strain: lineage3;lineage4.8

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 0.16
lineage4 Euro-American None 0.86
lineage4.8 Euro-American (mainly T) RD219 0.82
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA c.397_412dupATTGCCACCGATCATT Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide
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 7582 p.Asp94Gly missense_variant 0.78 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.87 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.76 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288829 c.397_412dupATTGCCACCGATCATT frameshift_variant 0.54 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.2 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.86 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 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491310 c.528C>T synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 0.18 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620854 p.Gly322Ser missense_variant 0.18 capreomycin
amikacin
kanamycin
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.8 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
nusG 734658 c.405A>G synonymous_variant 0.8 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.1 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.21 rifampicin 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 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.16 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302613 c.-318C>T upstream_gene_variant 0.17 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.78 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.11 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 0.22 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.27 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.87 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289365 c.-125delC upstream_gene_variant 0.17 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.24 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.1 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.91 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.18 cycloserine
Rv3236c 3612659 p.Ser153Leu missense_variant 0.17 pyrazinamide
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.86 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626081 p.Pro178Leu missense_variant 0.22 bedaquiline
rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.71 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.25 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.16 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.22 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246277 c.-237G>C upstream_gene_variant 0.28 ethambutol
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 0.16 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4407980 p.Pro75Ser missense_variant 0.19 streptomycin Uncertain significance