TB-Profiler result

Run: ERR4828339
Summary

Run ID: ERR4828339

Sample name:

Date: 2024-10-04T20:32:24.501190

Number of reads: 3198443

Percentage reads mapped: 99.26

Median coverage: 77.0

Strain: lineage1.1.1.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 0.93
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.11
lineage1 Indo-Oceanic RD239 0.92
lineage1.1.1 Indo-Oceanic RD239 0.92
lineage1.1.1.1 Indo-Oceanic RD239 0.91
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)
ethambutol
pyrazinamide
streptomycin gid c.87delC 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 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)
gid 4408115 c.87delC frameshift_variant 0.91 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 6112 p.Met291Ile missense_variant 1.0 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 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.93 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 0.89 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.9 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.86 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.81 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.94 pretomanid
delamanid Uncertain significance
clofazimine 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 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.88 ethionamide
hadA 731757 c.-173G>A upstream_gene_variant 0.96 isoniazid
hadA 731926 c.-4A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.95 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 0.89 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.89 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
mmpL5 778350 p.Ala44Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14 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 0.81 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin 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
embR 1417019 p.Cys110Tyr missense_variant 0.88 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.93 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.9 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474190 n.533C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid Uncertain significance
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834319 p.Val260Ile missense_variant 0.9 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.92 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.92 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 0.9 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.88 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 0.95 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.96 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
kasA 2518132 c.18C>T synonymous_variant 0.88 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.96 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.97 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.93 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.84 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878630 c.-124delC upstream_gene_variant 0.89 rifampicin Not assoc w R
clpC1 4038182 c.2523C>T synonymous_variant 0.88 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.88 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 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 4240031 p.Ala57Thr missense_variant 0.83 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.92 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.89 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.91 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.88 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.92 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.94 ethambutol Not assoc w R
embB 4248548 p.Ala679Ser missense_variant 0.94 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.16 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.85 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.87 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.9 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 0.89 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 0.91 streptomycin Not assoc w R