TB-Profiler result

Run: ERR13286094
Summary

Run ID: ERR13286094

Sample name:

Date: 2024-10-04T06:36:03.500721

Number of reads: 4432927

Percentage reads mapped: 99.62

Median coverage: 143.0

Strain: lineage1.2.2.2;lineage4.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.45
lineage1.2.2 Indo-Oceanic RD239 0.46
lineage1.2.2.2 Indo-Oceanic RD239 0.46
lineage4.1 Euro-American None 0.09
lineage4 Euro-American None 0.55
lineage1 Indo-Oceanic RD239 0.47
lineage4.3.3 Euro-American (LAM) RD115 0.46
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.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Arg154Gly Assoc w R
c.389delT Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine ald c.464delG Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.-11A>G Uncertain significance Mutation from literature
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 0.56 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.12 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1673432 c.-770T>A upstream_gene_variant 0.39 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid Assoc w R High-level resistance
pncA 2288782 p.Arg154Gly missense_variant 0.12 pyrazinamide Assoc w R
pncA 2288852 c.389delT frameshift_variant 0.42 pyrazinamide Assoc w R
ald 3087278 c.464delG frameshift_variant 0.15 cycloserine Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 0.11 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.42 ethambutol Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 0.47 ethionamide Uncertain significance 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 5075 c.-165C>T upstream_gene_variant 0.45 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 6835 c.-467C>T upstream_gene_variant 0.43 levofloxacin
moxifloxacin
gyrA 7268 c.-34C>T upstream_gene_variant 0.48 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 8040 p.Gly247Ser missense_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.41 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 0.59 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.44 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.39 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.43 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.52 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.14 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.42 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.45 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.47 rifampicin Not assoc w R
rpoC 763552 c.183C>T synonymous_variant 0.47 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.41 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.39 rifampicin Not assoc w R
rpoC 767123 p.Val1252Leu missense_variant 0.34 rifampicin Uncertain significance
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 0.51 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
rpsL 781435 c.-125G>C upstream_gene_variant 0.11 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.11 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.49 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.54 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 0.47 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.52 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.46 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471862 n.17T>G non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.52 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 0.5 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 0.5 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.39 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.49 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.49 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 0.48 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.49 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.41 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.43 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57 isoniazid
Rv2752c 3065824 p.Pro123Leu missense_variant 0.39 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.51 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.46 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.52 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 3626467 c.147G>A synonymous_variant 0.41 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
alr 3841356 p.Ser22Leu missense_variant 0.4 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.41 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.47 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.55 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 0.52 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.42 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245670 p.Ala813Gly missense_variant 0.32 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.42 ethambutol Not assoc w R
embB 4246979 p.Gly156Cys missense_variant 0.39 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.5 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.12 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.47 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.51 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.41 ethambutol Not assoc w R
ubiA 4269742 p.Leu31Pro missense_variant 0.49 ethambutol Uncertain significance
ethA 4326148 c.1326G>T synonymous_variant 0.52 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.54 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.47 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 0.44 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 0.4 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.57 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.59 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.39 streptomycin Not assoc w R