TB-Profiler result

Run: SRR25827375
Summary

Run ID: SRR25827375

Sample name:

Date: 2024-04-15T15:44:12.932027

Number of reads: 7948425

Percentage reads mapped: 98.32

Median coverage: 261.5

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 0.68
lineage2 East-Asian RD105 0.21
lineage1.2.2.2 Indo-Oceanic RD239 0.68
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.19
lineage2.2 East-Asian (Beijing) RD105;RD207 0.21
lineage1 Indo-Oceanic RD239 0.8
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
p.Gln853Pro Uncertain significance Mutation from literature
pyrazinamide pncA p.Asp63Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Tyr Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide
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 7581 p.Asp94Tyr missense_variant 0.19 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.26 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.15 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid Assoc w R High-level resistance
pncA 2289054 p.Asp63Ala missense_variant 0.17 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.33 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.2 ethambutol Assoc w R
embB 4249071 p.Gln853Pro missense_variant 0.24 ethambutol Uncertain significance Mutation from literature
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 0.7 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7283 c.-19G>T upstream_gene_variant 0.21 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 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.82 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 0.77 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.62 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Leu missense_variant 0.56 isoniazid
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.77 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 575907 p.Ala187Val missense_variant 0.19 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.17 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.21 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 0.77 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.78 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 0.82 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764666 p.Gly433Ser missense_variant 0.16 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 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22 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 0.21 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.75 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.75 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.78 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.8 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 0.76 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.71 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 0.62 pyrazinamide Uncertain significance
Rv1979c 2222159 c.1006C>T synonymous_variant 0.76 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78 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 0.69 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.77 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.77 isoniazid
ahpC 2726418 p.Glu76Lys missense_variant 0.61 isoniazid Uncertain significance
pepQ 2860365 c.54G>T synonymous_variant 0.22 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
thyA 3074069 p.Val135Phe missense_variant 0.16 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.75 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.82 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 0.71 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.22 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.68 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.78 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 0.81 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.73 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243217 c.-16C>A upstream_gene_variant 0.21 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.18 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.15 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.76 ethambutol Not assoc w R
embB 4247015 p.Ser168Ala missense_variant 0.21 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.82 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.22 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.17 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.74 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.79 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.69 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.75 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.86 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 0.8 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 4407848 p.Ala119Thr missense_variant 0.69 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.83 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.17 streptomycin Not assoc w R