TB-Profiler result

Run: SRR25827629
Summary

Run ID: SRR25827629

Sample name:

Date: 2024-10-05T13:27:55.603061

Number of reads: 6742512

Percentage reads mapped: 99.02

Median coverage: 234.0

Strain: lineage1.1.3.3;lineage2.2.1;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 0.3
lineage1.1.3 Indo-Oceanic RD239 0.36
lineage2 East-Asian RD105 0.33
lineage1.1.3.3 Indo-Oceanic RD239 0.37
lineage1.1 Indo-Oceanic RD239 0.35
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.32
lineage2.2 East-Asian (Beijing) RD105;RD207 0.32
lineage1 Indo-Oceanic RD239 0.36
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.Met306Val Assoc w R
pyrazinamide pncA p.Thr177Pro Assoc w R
c.390_391dupGG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.110delA Assoc w R
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 7570 p.Ala90Val missense_variant 0.23 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.34 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.37 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288713 p.Thr177Pro missense_variant 0.32 pyrazinamide Assoc w R
pncA 2288850 c.390_391dupGG frameshift_variant 0.34 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.34 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.59 ethambutol Assoc w R
ethA 4327363 c.110delA frameshift_variant 0.24 ethionamide 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 0.32 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 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.34 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 0.29 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.98 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.31 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.26 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.29 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.38 ethionamide
nusG 733858 c.-396C>T upstream_gene_variant 0.21 rifampicin
nusG 734116 c.-138T>C upstream_gene_variant 0.33 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.28 rifampicin Not assoc w R
rpoB 759940 p.Pro45Leu missense_variant 0.29 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.32 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.42 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.42 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.37 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.38 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.4 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 776006 c.2475C>T synonymous_variant 0.29 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.37 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776826 p.Glu552Gly missense_variant 0.26 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33 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 0.38 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 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 0.29 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.43 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.38 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.33 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.37 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.39 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 0.38 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2103062 c.-20C>T upstream_gene_variant 0.25 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 0.97 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.39 pyrazinamide Uncertain significance
PPE35 2168124 p.Gly830Glu missense_variant 0.36 pyrazinamide Uncertain significance
PPE35 2169630 p.Asn328Ser missense_variant 0.35 pyrazinamide Uncertain significance
PPE35 2169757 p.Asn286Asp missense_variant 0.37 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.34 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
pncA 2289365 c.-125delC upstream_gene_variant 0.27 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.34 isoniazid
kasA 2519100 p.Ala329Val missense_variant 0.34 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.3 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33 isoniazid Not assoc w R
folC 2747666 c.-68A>G upstream_gene_variant 0.37 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.34 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
Rv2681 2997944 c.1206C>T synonymous_variant 0.34 capreomycin Not assoc w R - Interim
Rv2752c 3064632 c.1560C>T synonymous_variant 0.33 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 0.38 ethionamide Uncertain significance
Rv3083 3449709 c.1206C>G synonymous_variant 0.38 ethionamide Not assoc w R - Interim
whiB7 3568425 c.255T>G synonymous_variant 0.16 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.31 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 0.34 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642877 p.Lys448Arg missense_variant 0.23 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
alr 3840493 c.928C>T synonymous_variant 0.35 cycloserine
alr 3841349 c.72C>A synonymous_variant 0.4 cycloserine
alr 3841362 p.Thr20Met missense_variant 0.35 cycloserine
clpC1 4040315 c.390G>A synonymous_variant 0.34 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.35 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.33 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.31 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 4138468 p.Thr430Ala missense_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4138622 c.1134C>T synonymous_variant 0.29 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
glpK 4139246 c.510C>T synonymous_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4239396 c.-467C>A upstream_gene_variant 0.35 ethambutol Uncertain significance
embC 4240207 c.345G>A synonymous_variant 0.35 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 0.31 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.33 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.34 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.29 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 0.31 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.43 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.39 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.15 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.28 ethambutol Not assoc w R
aftB 4267431 p.Ser469Leu missense_variant 0.32 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.37 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.41 ethambutol Not assoc w R
whiB6 4338208 p.Pro105Gln missense_variant 0.4 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 0.37 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
gid 4407588 c.615A>G synonymous_variant 0.97 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.27 streptomycin Not assoc w R
gid 4407766 p.Thr146Arg missense_variant 0.32 streptomycin Uncertain significance
gid 4407780 c.423G>A synonymous_variant 0.32 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.33 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.3 streptomycin Not assoc w R
gid 4408060 p.His48Arg missense_variant 0.28 streptomycin Uncertain significance