TB-Profiler result

Run: SRR26399247
Summary

Run ID: SRR26399247

Sample name:

Date: 2024-10-04T04:45:49.864507

Number of reads: 3090840

Percentage reads mapped: 99.43

Median coverage: 90.0

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.77
lineage1.1 Indo-Oceanic RD239 0.19
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage2.2 East-Asian (Beijing) RD105;RD207 0.8
lineage1 Indo-Oceanic RD239 0.22
lineage1.1.1 Indo-Oceanic RD239 0.2
lineage1.1.1.1 Indo-Oceanic RD239 0.21
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ala46Val Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
gid c.102delG 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 761139 p.His445Tyr missense_variant 0.23 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.56 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.42 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.4 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.79 isoniazid Assoc w R High-level resistance
pncA 2289105 p.Ala46Val missense_variant 0.38 pyrazinamide Assoc w R - Interim
embA 4243221 c.-12C>T upstream_gene_variant 0.8 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.43 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.24 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 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6762 p.Ala508Val missense_variant 0.23 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 8452 p.Ala384Val missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.16 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 13275 p.Tyr95Cys missense_variant 0.25 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.21 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.31 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.26 isoniazid Not assoc w R
fgd1 490922 p.Gln47Leu missense_variant 0.36 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 490972 p.Arg64Ser missense_variant 0.23 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.81 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576320 p.Val325Met missense_variant 0.27 isoniazid Uncertain significance
ethionamide Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.71 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.76 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.77 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.21 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.21 rifampicin Not assoc w R
nusG 734133 c.-121G>A upstream_gene_variant 0.18 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.14 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765065 p.Leu566Val missense_variant 0.28 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.21 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 776182 p.Asp767Asn missense_variant 0.75 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777581 p.Tyr300* stop_gained 0.16 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72 bedaquiline
clofazimine
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 1254543 c.-9T>G upstream_gene_variant 0.21 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.23 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.15 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.3 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.18 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.17 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 0.16 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.17 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156389 c.-278G>C upstream_gene_variant 0.21 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.26 pyrazinamide Uncertain significance
PPE35 2170749 c.-137A>G upstream_gene_variant 0.28 pyrazinamide
Rv1979c 2221889 p.Val426Ile missense_variant 0.46 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.24 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 0.33 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.19 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.26 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.17 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 3626562 p.Pro18Ser missense_variant 0.81 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.26 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.17 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 4139074 p.Leu228Val missense_variant 0.21 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.21 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.2 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.72 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.2 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.17 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.18 ethambutol Not assoc w R
embA 4246085 p.Glu951Asp missense_variant 0.58 ethambutol Not assoc w R
embB 4247509 p.Trp332Cys missense_variant 0.34 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.79 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.25 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 4338926 c.-405T>C upstream_gene_variant 0.41 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.18 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.79 streptomycin Not assoc w R