TB-Profiler result

Run: SRR25827857
Summary

Run ID: SRR25827857

Sample name:

Date: 2024-04-16T11:46:22.305895

Number of reads: 10238543

Percentage reads mapped: 98.86

Median coverage: 339.0

Strain: lineage1.1.2;lineage3

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 0.78
lineage1.1.2 Indo-Oceanic RD239 0.21
lineage1.1 Indo-Oceanic RD239 0.19
lineage1 Indo-Oceanic RD239 0.2
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 embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761155 p.Ser450Leu missense_variant 0.29 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.23 ethambutol Assoc w R
gid 4407851 c.351delG frameshift_variant 0.21 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 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6963 p.Arg575His missense_variant 0.43 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 9047 c.1746C>T synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.22 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 0.19 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
mshA 576000 p.Asp218Ala missense_variant 0.22 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.82 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.23 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.25 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.22 rifampicin Not assoc w R
rpoB 761074 p.Glu423Gly missense_variant 0.3 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.8 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 0.19 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.23 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 776181 p.Asp767Ala missense_variant 0.39 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776395 p.Phe696Leu missense_variant 0.24 clofazimine Not assoc w R
bedaquiline Uncertain significance
mmpL5 777444 p.Val346Ala missense_variant 0.47 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.2 linezolid Not assoc w R
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 0.19 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.2 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.22 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.23 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.26 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 0.18 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064758 c.-30A>G upstream_gene_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
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 0.23 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.26 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
pncA 2289365 c.-125delC upstream_gene_variant 0.83 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.27 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.8 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>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
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3065305 p.Ala296Val missense_variant 0.19 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.17 ethionamide Uncertain significance
Rv3083 3449722 p.Cys407Gly missense_variant 0.44 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.16 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
fbiA 3640618 p.Gly26Ser missense_variant 0.38 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiA 3640766 p.Pro75Leu missense_variant 0.27 clofazimine
pretomanid
delamanid
fbiB 3642877 p.Lys448Arg missense_variant 0.21 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
alr 3841046 c.375G>A synonymous_variant 0.2 cycloserine
alr 3841590 c.-170G>A upstream_gene_variant 0.47 cycloserine
ddn 3987057 p.Arg72Trp missense_variant 0.2 delamanid Uncertain significance
pretomanid
clpC1 4040517 p.Val63Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.18 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.8 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.15 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 0.83 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
glpK 4139246 c.510C>T synonymous_variant 0.2 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
glpK 4139250 p.Gly169Asp missense_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 0.19 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.2 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln 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 0.18 ethambutol Not assoc w R
embA 4243901 c.669G>A synonymous_variant 0.27 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.21 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.16 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.22 ethambutol Not assoc w R
aftB 4268719 p.Asn40Asp missense_variant 0.4 ethambutol Uncertain significance
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
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 0.23 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
gid 4407873 c.330G>T synonymous_variant 0.22 streptomycin Not assoc w R
gid 4408084 p.Glu40Gly missense_variant 0.29 streptomycin Uncertain significance
gid 4408251 c.-49T>C upstream_gene_variant 0.16 streptomycin Uncertain significance