TB-Profiler result

Run: ERR4799094
Summary

Run ID: ERR4799094

Sample name:

Date: 2024-10-05T03:13:12.020324

Number of reads: 7579267

Percentage reads mapped: 99.35

Median coverage: 202.0

Strain: lineage1.2.2.2;lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.92
lineage1.2.2.2 Indo-Oceanic RD239 0.9
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.05
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage1 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 rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
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 0.14 rifampicin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.11 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
embB 4247429 p.Met306Val missense_variant 0.14 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 5075 c.-165C>T upstream_gene_variant 0.9 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.88 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 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.89 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.9 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.9 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.92 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.92 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.93 rifampicin Not assoc w R
mmaA3 738201 c.-52G>T upstream_gene_variant 0.89 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.92 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.92 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 0.89 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
embR 1417019 p.Cys110Tyr missense_variant 0.9 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.9 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.94 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473021 n.1176G>A non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
tsnR 1853800 c.195G>A synonymous_variant 0.94 linezolid Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.93 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 0.94 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 0.91 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
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.88 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.9 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 0.93 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.9 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91 isoniazid
ahpC 2726418 p.Glu76Lys missense_variant 0.92 isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.9 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.89 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.91 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.9 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.91 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.86 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 0.87 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.91 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 0.11 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.89 ethambutol Not assoc w R
embB 4246430 c.-84C>T upstream_gene_variant 0.92 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.91 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.93 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 0.88 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.89 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.92 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 0.95 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 4407848 p.Ala119Thr missense_variant 0.92 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.92 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.1 streptomycin Not assoc w R