TB-Profiler result

Run: ERR13290498
Summary

Run ID: ERR13290498

Sample name:

Date: 2024-10-03T17:20:37.475839

Number of reads: 2695620

Percentage reads mapped: 99.12

Median coverage: 65.0

Strain: lineage1.1.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 0.88
lineage1 Indo-Oceanic RD239 0.95
lineage1.1.1 Indo-Oceanic RD239 0.96
lineage1.1.1.1 Indo-Oceanic RD239 0.96
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
pyrazinamide pncA p.His137Arg Not assoc w R - Interim Mutation from literature
streptomycin 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 0.98 rifampicin Assoc w R
rrs 1472750 n.905C>G non_coding_transcript_exon_variant 0.94 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 0.88 pyrazinamide Not assoc w R - Interim 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 6016 c.777C>T synonymous_variant 0.44 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.97 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 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.96 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 0.93 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.92 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.95 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.94 isoniazid Not assoc w R
fgd1 490972 p.Arg64Ser missense_variant 0.93 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.99 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574653 c.-695C>T upstream_gene_variant 0.96 isoniazid
ethionamide
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.95 ethionamide
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 764817 p.Val483Ala missense_variant 0.94 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.98 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.95 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.98 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 0.95 ethambutol Not assoc w R
embR 1417473 c.-126G>A upstream_gene_variant 0.98 ethambutol
embR 1417554 c.-207C>G upstream_gene_variant 0.98 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.96 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834319 p.Val260Ile missense_variant 0.98 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.97 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 0.95 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 0.99 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.94 pyrazinamide Uncertain significance
Rv1979c 2221786 p.Pro460Leu missense_variant 0.95 bedaquiline
clofazimine
Rv1979c 2222308 p.Asp286Gly missense_variant 0.94 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222842 c.322delG frameshift_variant 0.92 bedaquiline Uncertain significance
clofazimine Uncertain significance
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 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.97 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.98 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 0.95 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.98 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640394 c.-149_-148insT upstream_gene_variant 0.97 pretomanid
delamanid
clofazimine
rpoA 3878630 c.-124delC upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.95 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.95 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
glpK 4139602 p.Arg52Trp missense_variant 0.96 levofloxacin
moxifloxacin
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239652 c.-211T>G upstream_gene_variant 0.96 ethambutol Uncertain significance
embA 4244096 c.864C>T synonymous_variant 0.92 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.97 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.9 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.97 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 1.0 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 0.98 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 0.97 streptomycin Not assoc w R
gid 4407966 p.Leu79Phe missense_variant 0.98 streptomycin Uncertain significance