TB-Profiler result

Run: SRR25827479
Summary

Run ID: SRR25827479

Sample name:

Date: 2024-10-04T21:18:51.725992

Number of reads: 30903252

Percentage reads mapped: 99.39

Median coverage: 807.0

Strain: lineage1.2.2.2;lineage2.2.1

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.36
lineage2 East-Asian RD105 0.64
lineage1.2.2.2 Indo-Oceanic RD239 0.37
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.64
lineage2.2 East-Asian (Beijing) RD105;RD207 0.63
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.Val170Phe Assoc w R
p.Ser450Leu Assoc w R
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Asp328Gly Uncertain significance Mutation from literature
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.115delC 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.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
p.Ser94Ala Assoc w R - Interim
ethA c.672dupG Assoc w R
clofazimine
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
delamanid
bedaquiline atpE p.Ala63Pro Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
linezolid rrl n.2270G>T Assoc w R - Interim
n.2814G>T Assoc w R - Interim
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 0.67 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.Asp94Ala missense_variant 0.67 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)
rpoB 760314 p.Val170Phe missense_variant 0.36 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.66 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.65 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.64 streptomycin Assoc w R
atpE 1461231 p.Ala63Pro missense_variant 0.62 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
rrl 1475927 n.2270G>T non_coding_transcript_exon_variant 0.65 linezolid Assoc w R - Interim
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.63 linezolid Assoc w R - Interim
inhA 1673432 c.-770T>C upstream_gene_variant 0.34 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674481 p.Ser94Ala missense_variant 0.38 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.66 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.67 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.66 kanamycin Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.66 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.61 ethambutol Uncertain significance Mutation from literature
embB 4247496 p.Asp328Gly missense_variant 0.37 ethambutol Uncertain significance Mutation from literature
ethA 4326801 c.672dupG frameshift_variant 0.65 ethionamide Assoc w R
gid 4408087 c.115delC frameshift_variant 0.39 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 0.36 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.38 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 0.39 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.39 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 0.36 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.24 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.24 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.4 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.61 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
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 0.61 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.63 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.57 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.56 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.37 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.34 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 0.38 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.38 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.36 rifampicin Uncertain significance
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 0.67 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777431 c.1047_1049delCGC disruptive_inframe_deletion 0.35 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62 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 0.35 linezolid 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 0.66 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.34 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.37 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.39 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.67 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.34 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 0.4 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.31 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
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 0.36 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.15 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.13 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.37 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 2223553 c.-389C>A upstream_gene_variant 0.36 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.37 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.41 isoniazid
thyX 3067949 c.-4C>T upstream_gene_variant 0.67 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.4 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.64 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.35 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 3626467 c.147G>A synonymous_variant 0.35 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.65 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3627461 c.-848C>T upstream_gene_variant 0.34 rifampicin
bedaquiline
clpC1 4040517 p.Val63Ala missense_variant 0.33 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.34 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.39 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
embC 4240671 p.Thr270Ile missense_variant 0.35 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.66 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.35 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 0.6 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.38 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.25 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.17 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.15 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.15 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.18 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.16 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.17 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.41 ethambutol Not assoc w R
embB 4247847 p.Gln445Arg missense_variant 0.58 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.63 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.4 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.36 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.38 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.38 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.39 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.4 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338292 p.Ala77Val missense_variant 0.58 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 0.39 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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.63 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.35 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.35 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.64 streptomycin Not assoc w R