TB-Profiler result

Run: SRR1144811
Summary

Run ID: SRR1144811

Sample name:

Date: 2024-04-15T07:37:25.888367

Number of reads: 3709660

Percentage reads mapped: 99.28

Median coverage: 91.0

Strain: lineage1.1.1.1;lineage2.2.1.1

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 0.87
lineage1.1 Indo-Oceanic RD239 0.1
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.88
lineage2.2 East-Asian (Beijing) RD105;RD207 0.85
lineage1 Indo-Oceanic RD239 0.08
lineage1.1.1 Indo-Oceanic RD239 0.12
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.85
lineage1.1.1.1 Indo-Oceanic RD239 0.11
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.Met306Ile Assoc w R
pyrazinamide pncA p.His137Arg Not assoc w R - Interim Mutation from literature
p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.905C>G Uncertain significance Mutation from literature
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin Assoc w R
rrs 1472750 n.905C>G non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288832 p.His137Arg missense_variant 0.11 pyrazinamide Not assoc w R - Interim Mutation from literature
pncA 2289162 p.Leu27Pro missense_variant 0.9 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.8 ethambutol 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 0.11 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 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.2 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 0.23 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.21 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.19 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.13 clofazimine Uncertain significance
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 0.86 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.82 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.91 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.89 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.12 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.13 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.9 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.89 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.12 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid 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
fbiC 1302716 c.-215G>A upstream_gene_variant 0.85 clofazimine
pretomanid
delamanid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.16 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.15 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.13 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.86 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.11 pyrazinamide Uncertain significance
bacA 2062922 p.Ile603Val missense_variant 0.12 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.17 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154264 c.1848G>A synonymous_variant 0.92 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.8 amikacin Not assoc w R
kanamycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.11 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
thyX 3067954 c.-9G>A upstream_gene_variant 0.83 para-aminosalicylic_acid
thyA 3074141 p.Gln111* stop_gained 0.87 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.23 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.93 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.84 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640394 c.-149_-148insT upstream_gene_variant 0.14 clofazimine
pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.12 pyrazinamide Not assoc w R - Interim
glpK 4139602 p.Arg52Trp missense_variant 0.15 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239652 c.-211T>G upstream_gene_variant 0.21 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.91 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.81 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.17 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.12 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
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 0.77 streptomycin Not assoc w R
gid 4407966 p.Leu79Phe missense_variant 0.26 streptomycin Uncertain significance