TB-Profiler result

Run: ERR4796787
Summary

Run ID: ERR4796787

Sample name:

Date: 2024-03-26T18:27:38.025457

Number of reads: 5426414

Percentage reads mapped: 99.61

Median coverage: 132.0

Strain: lineage1.2.2.2;lineage3;lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.14
lineage1.2.2 Indo-Oceanic RD239 0.33
lineage1.2.2.2 Indo-Oceanic RD239 0.32
lineage4.4.1 Euro-American (S-type) None 0.55
lineage4 Euro-American None 0.48
lineage4.4.1.1 Euro-American None 0.53
lineage1 Indo-Oceanic RD239 0.37
lineage4.4 Euro-American None 0.52
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 embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ser104Arg Assoc w R
streptomycin gid c.102delG Assoc w R
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 0.44 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.53 isoniazid Assoc w R High-level resistance
pncA 2288932 p.Ser104Arg missense_variant 0.62 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.48 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.57 streptomycin 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 0.36 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.33 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 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.27 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 0.46 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.26 isoniazid Not assoc w R
Rv0010c 13637 c.-79C>T upstream_gene_variant 0.53 isoniazid Uncertain significance
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.38 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.37 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.21 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.31 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.42 rifampicin Not assoc w R
rpoB 759939 p.Pro45Ser missense_variant 0.42 rifampicin Uncertain significance
rpoB 762167 c.2361T>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.29 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.29 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775750 p.Gly911Ser missense_variant 0.45 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 0.53 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.28 linezolid Not assoc w R
Rv1129c 1253566 c.969A>G synonymous_variant 0.16 moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
Rv1129c 1254453 p.Glu28Gln missense_variant 0.43 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.5 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1416814 c.534G>A synonymous_variant 0.13 ethambutol Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.38 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.31 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.39 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473021 n.1176G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
inhA 1673658 c.-544G>A upstream_gene_variant 0.35 ethionamide
isoniazid
tsnR 1853974 c.369C>T synonymous_variant 0.24 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 0.21 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.41 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2102990 p.Val18Ala missense_variant 0.48 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154345 c.1767C>A synonymous_variant 0.58 isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.51 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.42 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.39 pyrazinamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.56 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.33 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.18 pyrazinamide Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.25 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.35 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.13 isoniazid Not assoc w R
ahpC 2726418 p.Glu76Lys missense_variant 0.36 isoniazid Uncertain significance
thyX 3067949 c.-4C>T upstream_gene_variant 0.47 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.53 ethionamide Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.3 ethionamide Uncertain significance
whiB7 3568857 c.-178C>T upstream_gene_variant 0.12 streptomycin Uncertain significance
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.49 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.43 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.4 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
ddn 3987057 p.Arg72Gly missense_variant 0.18 delamanid Uncertain significance
pretomanid
clpC1 4040517 p.Val63Ala missense_variant 0.38 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.42 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.15 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.24 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139633 c.123C>A synonymous_variant 0.24 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4238963 c.-900C>T upstream_gene_variant 0.48 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 4242075 p.Arg738Gln missense_variant 0.12 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243854 p.Leu208Phe missense_variant 0.51 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.38 ethambutol Not assoc w R
embB 4246430 c.-84C>T upstream_gene_variant 0.39 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.42 ethambutol Not assoc w R
aftB 4267925 c.912G>A synonymous_variant 0.53 ethambutol Not assoc w R - Interim
aftB 4267960 p.Val293Met missense_variant 0.38 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.41 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.34 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.4 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.38 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.37 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.48 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.48 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.51 streptomycin Not assoc w R