TB-Profiler result

Run: SRR25827459
Summary

Run ID: SRR25827459

Sample name:

Date: 2024-04-16T06:42:54.582730

Number of reads: 9636918

Percentage reads mapped: 98.83

Median coverage: 319.0

Strain: lineage1.2.2.2;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 0.77
lineage1.2.2 Indo-Oceanic RD239 0.19
lineage1.2.2.2 Indo-Oceanic RD239 0.22
lineage1 Indo-Oceanic RD239 0.22
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.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu116Pro Assoc w R - Interim
p.Phe13Ser Assoc w R
streptomycin gid p.Glu103* Assoc w R
c.115delC 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 ethA p.Met1? 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
gyrA 7582 p.Asp94Gly missense_variant 0.78 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288895 p.Leu116Pro missense_variant 0.78 pyrazinamide Assoc w R - Interim
pncA 2289204 p.Phe13Ser missense_variant 0.15 pyrazinamide Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 0.77 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.8 ethambutol Assoc w R
ethA 4327471 p.Met1? start_lost 0.82 ethionamide Assoc w R
gid 4407896 p.Glu103* stop_gained 0.83 streptomycin Assoc w R
gid 4408087 c.115delC frameshift_variant 0.29 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 5075 c.-165C>T upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 6490 c.-812T>G upstream_gene_variant 0.77 levofloxacin
moxifloxacin
gyrA 7268 c.-34C>T upstream_gene_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 0.27 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
gyrA 9596 c.2295G>T synonymous_variant 0.77 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13277 c.282T>C synonymous_variant 0.81 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.19 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.15 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.18 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.79 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.2 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.2 rifampicin Not assoc w R
nusG 734354 p.Pro34Leu missense_variant 0.77 rifampicin Not assoc w R
nusG 734753 p.Thr167Met missense_variant 0.74 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.8 rifampicin Not assoc w R
rpoB 761292 p.Val496Leu missense_variant 0.72 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.74 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 0.24 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.24 rifampicin Not assoc w R
rpoC 764181 p.Asp271Gly missense_variant 0.8 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.22 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776967 p.Gly505Asp missense_variant 0.23 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.19 linezolid Not assoc w R
Rv1129c 1254526 c.9G>T synonymous_variant 0.75 moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.21 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.22 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.21 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.21 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 0.2 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.23 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
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 2168742 p.Gly624Asp missense_variant 0.24 pyrazinamide Uncertain significance
PPE35 2170769 c.-157C>T upstream_gene_variant 0.78 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.23 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.24 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.79 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.21 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.22 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.78 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.77 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.18 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.25 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
alr 3840419 c.1002A>G synonymous_variant 0.22 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.23 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.75 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.29 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.8 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.19 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.17 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.8 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43G>C upstream_gene_variant 0.21 ethambutol Uncertain significance
embA 4245111 p.Val627Ile missense_variant 0.86 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.24 ethambutol Not assoc w R
embB 4247502 p.Phe330Ser missense_variant 0.25 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.26 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.19 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.2 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.24 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.19 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.2 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.31 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.21 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R