TB-Profiler result

Run: ERR13267130
Summary

Run ID: ERR13267130

Sample name:

Date: 2025-02-11T18:53:32.834311

Number of reads: 2369158

Percentage reads mapped: 99.5

Median coverage: 65.0

Strain: lineage1.1.3.1;lineage4.3.4.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.25
lineage1.1.3 Indo-Oceanic RD239 0.74
lineage1.1 Indo-Oceanic RD239 0.74
lineage4 Euro-American None 0.26
lineage1 Indo-Oceanic RD239 0.72
lineage1.1.3.1 Indo-Oceanic RD239 0.77
lineage4.3.4 Euro-American (LAM) RD174 0.26
lineage4.3.4.2 Euro-American (LAM) RD174 0.24
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
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 thyX c.-16C>T Mutation from literature
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 0.23 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid Assoc w R High-level resistance
thyX 3067961 c.-16C>T upstream_gene_variant 0.32 para-aminosalicylic_acid Mutation from literature
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 0.76 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 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.62 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 0.78 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.81 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.69 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 576733 c.1386C>T synonymous_variant 0.32 isoniazid
ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.73 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.75 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.69 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.77 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.77 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.77 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.72 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 0.7 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777572 c.909C>T synonymous_variant 0.77 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.65 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303584 c.654C>T synonymous_variant 0.71 pretomanid
delamanid
clofazimine
embR 1417019 p.Cys110Tyr missense_variant 0.75 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.84 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 0.82 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.77 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 0.71 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 0.62 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.65 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.64 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.6 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 0.5 isoniazid
kasA 2519191 c.1077G>A synonymous_variant 0.75 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.81 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 3065293 p.Val300Ala missense_variant 0.19 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.27 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.67 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.29 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.69 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841253 c.168C>T synonymous_variant 0.77 cycloserine
alr 3841277 c.144C>T synonymous_variant 0.74 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.3 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.78 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 4239763 c.-100C>T upstream_gene_variant 0.32 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.77 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.79 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 0.81 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.72 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.77 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.73 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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
whiB6 4338780 c.-259T>G upstream_gene_variant 0.55 kanamycin
capreomycin
amikacin
gid 4407554 c.649C>A synonymous_variant 0.69 streptomycin
gid 4407588 c.615A>G synonymous_variant 0.71 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.73 streptomycin Not assoc w R - Interim
gid 4407803 p.Ala134Pro missense_variant 0.3 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.69 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.26 streptomycin Not assoc w R