TB-Profiler result

Run: ERR163947
Summary

Run ID: ERR163947

Sample name:

Date: 2024-10-04T17:35:18.852238

Number of reads: 2721880

Percentage reads mapped: 99.16

Median coverage: 59.0

Strain: lineage1.1.2;lineage1.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.49
lineage1.2.2 Indo-Oceanic RD239 0.44
lineage1.2.2.2 Indo-Oceanic RD239 0.48
lineage1.1 Indo-Oceanic RD239 0.51
lineage1 Indo-Oceanic RD239 0.97
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
isoniazid inhA p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin rrs n.514A>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
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 761139 p.His445Asn missense_variant 0.47 rifampicin Assoc w R
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance Mutation from literature
inhA 1674481 p.Ser94Ala missense_variant 0.48 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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 0.29 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.31 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 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.99 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 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.87 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.42 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.97 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.97 ethionamide
hadA 732154 c.225G>C synonymous_variant 0.66 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.97 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 763552 c.183C>T synonymous_variant 0.44 rifampicin Not assoc w R
rpoC 763790 p.Glu141Lys missense_variant 0.68 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.95 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.57 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 800250 c.-559C>G upstream_gene_variant 0.47 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.96 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.96 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 1.0 ethambutol Not assoc w R
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
tsnR 1853974 c.369C>T synonymous_variant 0.98 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.47 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 0.99 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.38 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155746 c.366C>T synonymous_variant 0.5 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.56 pyrazinamide Uncertain significance
PPE35 2168742 p.Gly624Asp missense_variant 0.59 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.33 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.98 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.46 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.5 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 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.96 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 3626158 c.456C>T synonymous_variant 0.39 rifampicin
bedaquiline
mtrB 3626467 c.147G>A synonymous_variant 0.38 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4038328 p.Glu793Gln missense_variant 0.45 pyrazinamide Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.97 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.4 pyrazinamide Uncertain significance
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 4240671 p.Thr270Ile missense_variant 0.99 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.97 ethambutol Not assoc w R
embC 4242559 c.2697G>A synonymous_variant 0.62 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.48 ethambutol Not assoc w R
embA 4245670 p.Ala813Gly missense_variant 0.48 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.97 ethambutol Not assoc w R
embB 4246979 p.Gly156Cys missense_variant 0.56 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.92 ethambutol Not assoc w R
embB 4249654 p.His1047Gln missense_variant 0.6 ethambutol
embB 4249673 p.Ser1054Pro missense_variant 0.53 ethambutol Not assoc w R - Interim
aftB 4267960 p.Val293Met missense_variant 0.38 ethambutol Uncertain significance
ubiA 4269162 p.Leu224Phe missense_variant 0.39 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.97 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.94 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.49 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.37 ethionamide Uncertain significance
ethA 4328209 c.-736C>A upstream_gene_variant 0.67 ethionamide
whiB6 4338203 p.Arg107Cys missense_variant 0.59 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 1.0 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 0.98 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.41 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.97 streptomycin Not assoc w R
gid 4407935 p.Leu90Val missense_variant 0.62 streptomycin Uncertain significance
gid 4407944 p.Gln87Glu missense_variant 0.65 streptomycin Uncertain significance