TB-Profiler result

Run: ERR4596934
Summary

Run ID: ERR4596934

Sample name:

Date: 2024-10-03T15:29:40.881572

Number of reads: 4645839

Percentage reads mapped: 99.47

Median coverage: 140.0

Strain: lineage1.1.2;lineage3.1.1

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 0.76
lineage1.1.2 Indo-Oceanic RD239 0.23
lineage3.1.1 East-African-Indian RD750 0.79
lineage1.1 Indo-Oceanic RD239 0.21
lineage1 Indo-Oceanic RD239 0.21
lineage3.1 East-African-Indian RD750 0.74
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
p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
p.Ser315Asn Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Val128Gly Assoc w R
streptomycin gid c.471delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1265_1266insT Assoc w R
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 761155 p.Ser450Leu missense_variant 0.8 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.21 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Asn missense_variant 0.33 isoniazid Assoc w R High-level resistance
pncA 2288859 p.Val128Gly missense_variant 0.84 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.16 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.78 ethambutol Assoc w R
ethA 4326208 c.1265_1266insT frameshift_variant 0.74 ethionamide Assoc w R
gid 4407731 c.471delG frameshift_variant 0.72 streptomycin 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 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.19 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 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.25 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 0.22 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.22 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.97 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.29 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.27 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.75 rifampicin Not assoc w R
rpoB 761407 p.Val534Ala missense_variant 0.76 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.7 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.16 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.21 rifampicin Not assoc w R
rpoC 765988 c.2619G>A synonymous_variant 0.24 rifampicin Not assoc w R - Interim
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 0.99 bedaquiline Not assoc w R - Interim
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 0.16 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 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 0.25 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.17 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.27 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.22 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.2 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 0.24 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 0.99 isoniazid Not assoc w R
katG 2155383 c.729C>T synonymous_variant 0.21 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.97 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.2 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.77 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.21 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
Rv1979c 2223550 c.-386C>T upstream_gene_variant 0.26 bedaquiline Uncertain significance
clofazimine Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.75 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.19 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.21 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.78 isoniazid Not assoc w R
ahpC 2726468 c.276G>A synonymous_variant 0.31 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.73 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
ribD 2986645 c.-194G>A upstream_gene_variant 0.23 para-aminosalicylic_acid
Rv2681 2996912 c.174C>T synonymous_variant 0.23 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.25 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 3065951 p.His81Tyr missense_variant 0.24 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyX 3067491 p.Ala152Val missense_variant 0.2 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.29 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.24 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640446 c.-97A>T upstream_gene_variant 0.24 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
clpC1 4040036 c.669C>T synonymous_variant 0.22 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.27 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.81 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.14 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 0.78 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 4240172 p.Val104Met missense_variant 0.72 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.24 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.24 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.88 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.76 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243323 p.Val31Ile missense_variant 0.77 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.19 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.27 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.18 ethambutol Not assoc w R
ethR 4328051 p.Ala168Val missense_variant 0.75 ethionamide
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 0.24 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 0.79 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.15 streptomycin Not assoc w R