TB-Profiler result

Run: SRR25827865
Summary

Run ID: SRR25827865

Sample name:

Date: 2024-10-05T00:01:58.049135

Number of reads: 9573725

Percentage reads mapped: 99.04

Median coverage: 330.0

Strain: lineage1.1.2;lineage3

Spoligotype:

Drug-resistance: Pre-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 0.16
lineage1.1.2 Indo-Oceanic RD239 0.83
lineage1.1 Indo-Oceanic RD239 0.83
lineage1 Indo-Oceanic RD239 0.83
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
ethambutol embB p.Tyr319Ser Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.18 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.17 rifampicin Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.18 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 0.83 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 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.85 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 0.82 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.79 isoniazid Not assoc w R
Rv0010c 13905 c.-347G>T upstream_gene_variant 0.17 isoniazid
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.81 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.14 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.82 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 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.82 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 0.86 rifampicin Not assoc w R
rpoC 766446 p.Gly1026Ala missense_variant 0.17 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.81 bedaquiline Uncertain significance
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.84 linezolid Not assoc w R
Rv1129c 1253952 p.Ala195Pro missense_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
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
sigE 1364397 c.-16C>T upstream_gene_variant 0.8 pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.85 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.87 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.86 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476685 n.3028A>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
tsnR 1853974 c.369C>T synonymous_variant 0.87 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.87 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 0.86 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 0.89 pyrazinamide Uncertain significance
PPE35 2170173 p.Asp147Ala missense_variant 0.81 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.87 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 2289365 c.-125delC upstream_gene_variant 0.14 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.77 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.84 isoniazid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.18 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 2784211 c.-169A>C upstream_gene_variant 0.3 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2681 2996912 c.174C>T synonymous_variant 0.84 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.82 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
ald 3087862 p.Gly348Glu missense_variant 0.16 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.82 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.85 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 0.83 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.83 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.78 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.15 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.82 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
embC 4240671 p.Thr270Ile missense_variant 0.81 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.84 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.18 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 0.83 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.14 ethambutol Not assoc w R - Interim
embA 4245218 c.1986C>T synonymous_variant 0.84 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.81 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.84 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.83 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.84 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.84 ethambutol Not assoc w R
ethA 4326453 p.Ala341Thr missense_variant 0.17 ethionamide
whiB6 4338194 p.Arg110Trp missense_variant 0.16 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 0.81 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 0.81 streptomycin Not assoc w R