TB-Profiler result

Run: SRR25827445
Summary

Run ID: SRR25827445

Sample name:

Date: 2024-10-03T14:40:40.806278

Number of reads: 7331874

Percentage reads mapped: 98.78

Median coverage: 245.0

Strain: lineage1.1.2;lineage3

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 0.45
lineage1.1.2 Indo-Oceanic RD239 0.53
lineage1.1 Indo-Oceanic RD239 0.53
lineage1 Indo-Oceanic RD239 0.52
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
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
rpoB 761161 p.Leu452Pro missense_variant 0.49 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Leu missense_variant 0.56 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
gyrB 6112 p.Met291Ile missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.51 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 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9047 c.1746C>T synonymous_variant 0.53 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.54 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
gyrA 9443 c.2142G>A synonymous_variant 0.56 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.5 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.39 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
mshA 576000 p.Asp218Ala missense_variant 0.53 isoniazid Not assoc w R - Interim
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.42 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.5 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.51 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.51 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.52 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.52 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.4 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 0.53 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 776395 p.Phe696Leu missense_variant 0.54 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpR5 779261 p.Thr91Ile missense_variant 0.51 bedaquiline Uncertain significance
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.48 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
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.48 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.5 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.49 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472485 n.640G>A non_coding_transcript_exon_variant 0.51 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476436 n.2779A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.55 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.5 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 0.57 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 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.49 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.58 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
pncA 2289047 c.195C>T synonymous_variant 0.47 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.51 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.54 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.48 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.48 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.43 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 2783854 c.189C>T synonymous_variant 0.55 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2681 2996912 c.174C>T synonymous_variant 0.59 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.53 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 3065305 p.Ala296Val missense_variant 0.52 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3065748 p.His148Gln missense_variant 0.55 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087583 c.768_769dupGC frameshift_variant 0.5 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.53 ethionamide Uncertain significance
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
mtrB 3626467 c.147G>A synonymous_variant 0.52 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.53 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.5 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.42 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.46 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 0.41 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 4240671 p.Thr270Ile missense_variant 0.53 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.56 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.42 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 0.49 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.18 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.52 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.5 ethambutol Not assoc w R
aftB 4269096 c.-260C>G upstream_gene_variant 0.38 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.49 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.45 ethambutol Not assoc w R
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 0.47 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 0.5 streptomycin Not assoc w R
gid 4407980 p.Pro75Ser missense_variant 0.53 streptomycin Uncertain significance