TB-Profiler result

Run: SRR19428616
Summary

Run ID: SRR19428616

Sample name:

Date: 2024-10-04T00:39:00.250805

Number of reads: 2815830

Percentage reads mapped: 99.36

Median coverage: 138.0

Strain: lineage1.1.2;lineage3.1.1

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 0.2
lineage1.1.2 Indo-Oceanic RD239 0.81
lineage3.1.1 East-African-Indian RD750 0.24
lineage1.1 Indo-Oceanic RD239 0.77
lineage1 Indo-Oceanic RD239 0.77
lineage3.1 East-African-Indian RD750 0.16
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
gyrB 6112 p.Met291Ile missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.77 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 0.81 isoniazid Not assoc w R
Rv0010c 13304 c.255G>A synonymous_variant 0.8 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.78 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 0.21 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.76 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.82 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.75 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.15 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.71 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.21 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 0.8 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.82 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.8 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 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.79 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpR5 779303 p.Arg105His missense_variant 0.86 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.82 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
fbiC 1303051 p.Val41Met missense_variant 0.69 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.76 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.76 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.79 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.79 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.75 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 0.72 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.84 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.25 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.75 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223136 p.Ala10Val missense_variant 0.73 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223200 c.-36G>A upstream_gene_variant 0.81 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.24 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.71 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86 isoniazid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.2 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
Rv2477c 2782508 p.Trp512Ser missense_variant 0.78 kanamycin
levofloxacin
moxifloxacin
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin
Rv2680 2996003 c.-101_-50delGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN upstream_gene_variant 0.96 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.8 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.8 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.79 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.82 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.82 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.74 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.25 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.75 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 0.21 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 4239593 c.-270G>A upstream_gene_variant 0.82 ethambutol Not assoc w R
embC 4240172 p.Val104Met missense_variant 0.23 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.88 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.78 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.25 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.24 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.82 ethambutol Not assoc w R
embA 4244167 p.Ala312Val missense_variant 0.75 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.73 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.75 ethambutol Not assoc w R
embB 4249439 p.Glu976Lys missense_variant 0.16 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.79 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.78 ethambutol Not assoc w R
ethA 4326432 p.Leu348Phe missense_variant 0.79 ethionamide 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 0.88 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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.2 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.79 streptomycin Not assoc w R