TB-Profiler result

Run: ERR4831734
Summary

Run ID: ERR4831734

Sample name:

Date: 2024-10-04T21:54:34.779641

Number of reads: 2692422

Percentage reads mapped: 99.53

Median coverage: 88.0

Strain: lineage1.1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: HR-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 0.15
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.85
lineage2.2 East-Asian (Beijing) RD105;RD207 0.86
lineage1 Indo-Oceanic RD239 0.17
lineage1.1.1 Indo-Oceanic RD239 0.15
lineage1.1.1.1 Indo-Oceanic RD239 0.14
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Gly Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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
rpsL 781687 p.Lys43Arg missense_variant 0.91 streptomycin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.83 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155169 p.Ser315Gly missense_variant 0.89 isoniazid Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.86 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 0.15 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 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.11 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 0.14 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.16 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.12 isoniazid Not assoc w R
Rv0010c 13631 c.-73T>C upstream_gene_variant 0.21 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.88 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.81 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.11 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.12 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763272 c.3466C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763884 p.Ala172Val missense_variant 0.12 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.13 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 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82 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 0.14 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 0.87 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.17 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
inhA 1674687 c.486G>A synonymous_variant 0.16 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
rpsA 1834177 c.636A>C synonymous_variant 0.82 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.15 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.12 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 2063106 c.1623G>A synonymous_variant 0.15 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin 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 2167983 p.Gly877Asp missense_variant 0.16 pyrazinamide Uncertain significance
PPE35 2170177 p.Leu146Val missense_variant 0.15 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726051 c.-142G>A upstream_gene_variant 0.19 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.17 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
Rv2752c 3065129 c.1063C>T synonymous_variant 0.83 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612037 p.Phe360Leu missense_variant 0.8 pyrazinamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.12 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 0.96 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878971 c.-464C>T upstream_gene_variant 0.22 rifampicin
clpC1 4039869 p.Arg279Leu missense_variant 0.22 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.14 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.2 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 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.86 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.19 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.16 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.93 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.16 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.11 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.92 ethionamide Uncertain significance
whiB6 4338242 p.Gln94Glu missense_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338579 c.-58C>T upstream_gene_variant 0.11 kanamycin
capreomycin
amikacin
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 0.12 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 4407873 c.330G>T synonymous_variant 0.14 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.91 streptomycin Not assoc w R