TB-Profiler result

Run: SRR25340766
Summary

Run ID: SRR25340766

Sample name:

Date: 2024-10-05T09:25:19.946359

Number of reads: 5707461

Percentage reads mapped: 99.29

Median coverage: 166.0

Strain: lineage1.1.2;lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.49
lineage1.1.2 Indo-Oceanic RD239 0.51
lineage1.1 Indo-Oceanic RD239 0.49
lineage1 Indo-Oceanic RD239 0.51
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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
dnaA 1519 p.Arg507Cys missense_variant 0.34 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.44 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6963 p.Arg575His missense_variant 0.64 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 8452 p.Ala384Val missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.43 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 13298 p.Ile87Met missense_variant 0.49 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.43 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
Rv0565c 657081 c.390G>A synonymous_variant 0.52 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.45 ethionamide
nusG 733916 c.-338A>C upstream_gene_variant 0.44 rifampicin
nusG 734116 c.-138T>C upstream_gene_variant 0.54 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.58 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.51 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.52 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.44 rifampicin Not assoc w R
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 776181 p.Asp767Ala missense_variant 0.48 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.44 linezolid Not assoc w R
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
Rv1258c 1406503 p.Val280Leu missense_variant 0.47 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.44 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.46 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.53 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.54 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.53 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.63 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154674 p.Ala480Ser missense_variant 0.43 isoniazid Uncertain significance
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 2167983 p.Gly877Asp missense_variant 0.47 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.48 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
Rv1979c 2223685 c.-521G>A upstream_gene_variant 0.46 bedaquiline
clofazimine
pncA 2289365 c.-125delC upstream_gene_variant 0.54 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.55 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.32 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.63 isoniazid Not assoc w R
ahpC 2726117 c.-76T>A upstream_gene_variant 0.61 isoniazid Uncertain significance
Rv2477c 2782498 c.1545C>T synonymous_variant 0.5 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
Rv2681 2996912 c.174C>T synonymous_variant 0.53 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3065538 c.654G>A synonymous_variant 0.48 levofloxacin
moxifloxacin
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 3448714 p.Asp71His missense_variant 0.6 ethionamide Uncertain significance
Rv3236c 3613116 p.Val1Met missense_variant 0.43 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.53 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640656 p.Asp38Glu missense_variant 0.63 pretomanid
delamanid
clofazimine
alr 3841590 c.-170G>A upstream_gene_variant 0.56 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.51 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.53 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.5 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 4138622 c.1134C>T synonymous_variant 0.57 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 4240483 c.621G>C synonymous_variant 0.49 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.56 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.59 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.51 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.54 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.52 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.59 ethambutol Not assoc w R
aftB 4268156 c.681C>T synonymous_variant 0.54 ethambutol Not assoc w R - Interim
aftB 4268719 p.Asn40Asp missense_variant 0.4 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.52 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.5 ethambutol Not assoc w R
whiB6 4338224 c.297delC frameshift_variant 0.61 kanamycin Uncertain significance
capreomycin Uncertain significance
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 4338603 c.-82C>T upstream_gene_variant 0.49 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 4407873 c.330G>T synonymous_variant 0.46 streptomycin Not assoc w R
gid 4407979 p.Pro75Leu missense_variant 0.48 streptomycin Uncertain significance