TB-Profiler result

Run: SRR28351431
Summary

Run ID: SRR28351431

Sample name:

Date: 2024-10-03T17:03:04.012615

Number of reads: 5689860

Percentage reads mapped: 99.86

Median coverage: 167.0

Strain: lineage1.1.2

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
lineage1.1.2 Indo-Oceanic RD239 0.95
lineage1.1 Indo-Oceanic RD239 0.94
lineage1 Indo-Oceanic RD239 0.96
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 embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Leu Assoc w R
pyrazinamide pncA p.Leu156Pro Uncertain significance Mutation from literature
streptomycin rrs n.517C>T Assoc w R
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 0.94 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.94 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2288775 p.Leu156Pro missense_variant 0.95 pyrazinamide Uncertain significance Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.82 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.87 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 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.96 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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9125 c.1824C>T synonymous_variant 0.94 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.97 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.9 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 657578 c.-108T>C upstream_gene_variant 0.94 ethionamide
nusG 734066 c.-188G>A upstream_gene_variant 0.92 rifampicin Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.92 rifampicin Not assoc w R
nusG 734118 c.-136C>T upstream_gene_variant 0.92 rifampicin Uncertain significance
rpoB 759546 c.-261A>G upstream_gene_variant 0.94 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.95 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 0.95 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.95 rifampicin Not assoc w R
rpoC 764843 p.Ala492Pro missense_variant 0.9 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.96 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 0.95 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 0.93 linezolid Not assoc w R
Rv1129c 1253841 p.Trp232Gly missense_variant 0.94 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
embR 1417019 p.Cys110Tyr missense_variant 0.91 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.89 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.95 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.96 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.89 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 0.94 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 0.95 pyrazinamide Uncertain significance
PPE35 2170726 c.-114G>A upstream_gene_variant 0.93 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.94 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
kasA 2518132 c.18C>T synonymous_variant 0.93 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.94 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.93 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
thyA 3074595 c.-124C>A upstream_gene_variant 0.91 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.97 ethionamide Uncertain significance
whiB7 3568732 c.-53C>T upstream_gene_variant 0.94 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.94 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 0.93 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.96 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.95 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.97 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 0.89 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.93 ethambutol Not assoc w R
embC 4241848 c.1986C>G synonymous_variant 0.14 ethambutol
embC 4242075 p.Arg738Gln missense_variant 0.17 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 0.85 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.87 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.78 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.92 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.97 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.92 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 0.94 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 4338945 c.-424C>T upstream_gene_variant 0.95 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.96 streptomycin Not assoc w R