TB-Profiler result

Run: ERR4797196
Summary

Run ID: ERR4797196

Sample name:

Date: 2024-10-03T15:30:41.393713

Number of reads: 6003607

Percentage reads mapped: 99.58

Median coverage: 179.0

Strain: lineage1.2.2.2;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 0.59
lineage1.2.2 Indo-Oceanic RD239 0.4
lineage1.2.2.2 Indo-Oceanic RD239 0.38
lineage4 Euro-American None 0.62
lineage1 Indo-Oceanic RD239 0.39
lineage4.3.3 Euro-American (LAM) RD115 0.61
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Thr135Pro Assoc w R
streptomycin gid p.Pro75Arg Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 0.66 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.63 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)
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid Assoc w R High-level resistance
pncA 2288839 p.Thr135Pro missense_variant 0.66 pyrazinamide Assoc w R
gid 4407979 p.Pro75Arg missense_variant 0.56 streptomycin 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 0.4 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.43 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 0.6 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.43 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 0.45 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.26 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.27 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.38 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.43 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.4 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.42 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.39 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.39 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.62 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 0.33 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 0.43 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406645 p.Asp232Glu missense_variant 0.34 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.62 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.47 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.33 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.44 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674712 p.Val171Ile missense_variant 0.37 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 0.65 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.48 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 0.36 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063823 c.905delT frameshift_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.44 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.66 isoniazid Not assoc w R
katG 2156235 c.-124G>A upstream_gene_variant 0.66 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.4 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.36 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.38 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
pncA 2289366 c.-125C>T upstream_gene_variant 0.38 pyrazinamide
pncA 2290198 c.-957C>T upstream_gene_variant 0.52 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.39 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.68 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.44 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.6 para-aminosalicylic_acid
Rv2681 2997777 p.Ala347Thr missense_variant 0.32 capreomycin Uncertain significance
thyX 3067954 c.-9G>A upstream_gene_variant 0.56 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.61 para-aminosalicylic_acid
thyA 3074096 p.Arg126Gly missense_variant 0.62 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.34 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.45 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 0.4 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626567 p.Ser16Tyr missense_variant 0.35 rifampicin Uncertain significance
bedaquiline Uncertain significance
alr 3840402 p.Arg340Leu missense_variant 0.42 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.6 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.4 pyrazinamide Not assoc w R - Interim
panD 4045025 c.-744C>A upstream_gene_variant 0.44 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.33 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 0.37 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.46 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.49 ethambutol Not assoc w R
embB 4247629 c.1116C>T synonymous_variant 0.46 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.49 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.44 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.37 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.4 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.48 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.42 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 0.35 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 0.39 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.4 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.62 streptomycin Not assoc w R