TB-Profiler result

Run: SRR25827646
Summary

Run ID: SRR25827646

Sample name:

Date: 2024-04-14T13:47:20.781581

Number of reads: 7769926

Percentage reads mapped: 98.39

Median coverage: 261.0

Strain: lineage1.2.2.2;lineage2.2.1

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
lineage1.2.2 Indo-Oceanic RD239 0.71
lineage2 East-Asian RD105 0.28
lineage1.2.2.2 Indo-Oceanic RD239 0.72
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.27
lineage2.2 East-Asian (Beijing) RD105;RD207 0.28
lineage1 Indo-Oceanic RD239 0.71
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
p.Ser450Leu Assoc w R
p.Leu452Pro Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. 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
p.Trp191Arg Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.102delG 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.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 7570 p.Ala90Val missense_variant 0.7 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 7581 p.Asp94Asn missense_variant 0.3 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asn missense_variant 0.62 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.66 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.26 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.32 isoniazid Assoc w R High-level resistance
katG 2155541 p.Trp191Arg missense_variant 0.34 isoniazid Uncertain significance Mutation from literature
pncA 2288847 p.Gly132Ala missense_variant 0.3 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.71 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.28 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.72 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 0.75 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.75 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.66 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 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.64 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 0.75 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.56 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Leu missense_variant 0.56 isoniazid
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.7 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.25 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.27 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576651 p.Asp435Ala missense_variant 0.19 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.29 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.27 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.24 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.67 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.75 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 0.73 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.3 rifampicin Uncertain significance
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 776182 p.Asp767Asn missense_variant 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26 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 0.73 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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.27 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.66 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.72 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.71 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473000 n.1155G>A non_coding_transcript_exon_variant 0.67 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.67 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 0.7 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101931 p.Ala371Val missense_variant 0.69 ethionamide
delamanid
isoniazid Uncertain significance
ndh 2102240 p.Arg268His missense_variant 0.73 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 0.79 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.74 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 0.74 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.71 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.71 isoniazid
ahpC 2726418 p.Glu76Lys missense_variant 0.73 isoniazid Uncertain significance
Rv2752c 3064700 p.Ser498Pro missense_variant 0.3 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086791 c.-29T>C upstream_gene_variant 0.39 cycloserine
ald 3087535 c.718dupC frameshift_variant 0.22 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.68 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.75 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 0.72 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.34 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.73 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.76 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.74 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
embC 4240671 p.Thr270Ile missense_variant 0.74 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.33 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.67 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 0.32 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.75 ethambutol Not assoc w R - Interim
embA 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.74 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.68 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.21 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.72 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.75 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.69 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.68 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.67 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.76 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 0.81 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 4407620 p.Tyr195His missense_variant 0.3 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.7 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.73 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.26 streptomycin Not assoc w R