TB-Profiler result

Run: SRR25827313
Summary

Run ID: SRR25827313

Sample name:

Date: 2024-04-15T06:10:02.939275

Number of reads: 3744788

Percentage reads mapped: 49.89

Median coverage: 104.0

Strain: lineage3;lineage4.8

Spoligotype:

Drug-resistance: 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 0.2
lineage4 Euro-American None 0.81
lineage4.8 Euro-American (mainly T) RD219 0.78
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
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Tyr 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 ethA c.385dupC Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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 7581 p.Asp94Tyr missense_variant 0.8 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.78 linezolid Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.88 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.79 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.8 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.78 ethambutol Assoc w R
ethA 4327088 c.385dupC frameshift_variant 0.78 ethionamide 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 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9666 p.Arg789Gly missense_variant 0.3 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 490671 c.-112A>G upstream_gene_variant 0.81 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 0.18 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.79 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.26 ethionamide Not assoc w R - Interim
nusG 734658 c.405A>G synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 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 0.18 rifampicin Not assoc w R
rpoC 765730 c.2361G>A synonymous_variant 0.25 rifampicin
rpoC 766494 p.Gly1042Asp missense_variant 0.79 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 0.18 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 0.21 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406472 p.Thr290Ile missense_variant 0.72 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.72 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475952 n.2295A>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.15 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.22 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2168957 c.1656G>A synonymous_variant 0.19 pyrazinamide 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
pncA 2289365 c.-125delC upstream_gene_variant 0.18 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.2 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.24 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 0.8 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
ald 3087398 c.580dupG frameshift_variant 0.7 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.32 streptomycin
amikacin
kanamycin
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.81 pyrazinamide Not assoc w R
lpqB 3623190 p.Val574Ala missense_variant 0.21 bedaquiline
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.22 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.84 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.14 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.21 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
glpK 4139246 c.510C>T synonymous_variant 0.24 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.29 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
gid 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4407973 p.Val77Gly missense_variant 0.72 streptomycin Uncertain significance