TB-Profiler result

Run: SRR29096312
Summary

Run ID: SRR29096312

Sample name:

Date: 2024-10-04T04:51:39.974923

Number of reads: 2746624

Percentage reads mapped: 99.49

Median coverage: 93.0

Strain: lineage3.1.1;lineage4.6.3

Spoligotype:

Drug-resistance: MDR-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 0.5
lineage4.6 Euro-American None 0.48
lineage3.1.1 East-African-Indian RD750 0.51
lineage4.6.3 Euro-American None 0.49
lineage4 Euro-American None 0.52
lineage3.1 East-African-Indian RD750 0.5
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.Gln497Arg Assoc w R
pyrazinamide pncA p.Trp119Arg Assoc w R - Interim
streptomycin rrs n.906A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid Assoc w R High-level resistance
pncA 2288887 p.Trp119Arg missense_variant 0.62 pyrazinamide Assoc w R - Interim
embB 4248003 p.Gln497Arg missense_variant 0.51 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 8049 p.Ser250Ala missense_variant 0.59 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13533 p.Arg9His missense_variant 0.49 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.46 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620072 p.Pro61Leu missense_variant 0.58 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.58 ethionamide Not assoc w R - Interim
nusG 734562 c.309G>A synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.59 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.55 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.53 rifampicin Not assoc w R
rpoC 765462 p.Asn698Ser missense_variant 0.59 rifampicin Uncertain significance
rpoC 765519 p.Lys717Thr missense_variant 0.57 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 0.53 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776987 c.1493delC frameshift_variant 0.43 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 778673 p.Pro78Leu missense_variant 0.53 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.52 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
bacA 2064376 p.Val118Ala missense_variant 0.6 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.53 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.49 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.47 pyrazinamide 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
pncA 2289047 c.195C>T synonymous_variant 0.6 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.52 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.51 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.53 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
pepQ 2860371 c.48C>T synonymous_variant 0.59 bedaquiline
clofazimine
ald 3086788 c.-32T>C upstream_gene_variant 0.45 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.46 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3640824 c.-711C>A upstream_gene_variant 0.57 pretomanid
delamanid
clofazimine
panD 4044872 c.-591C>T upstream_gene_variant 0.43 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240172 p.Val104Met missense_variant 0.52 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.56 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.51 ethambutol Not assoc w R
embC 4242185 p.Asp775Asn missense_variant 0.42 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
aftB 4268573 p.Met88Ile missense_variant 0.46 ethambutol Uncertain significance
ubiA 4269162 p.Leu224Phe missense_variant 0.52 ethambutol Uncertain significance
whiB6 4338268 p.Gly85Ala missense_variant 0.45 kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
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 4338635 c.-114A>G upstream_gene_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.51 streptomycin Not assoc w R
gid 4407934 p.Leu90Arg missense_variant 0.52 streptomycin Uncertain significance