TB-Profiler result

Run: ERR4799036
Summary

Run ID: ERR4799036

Sample name:

Date: 2024-04-14T23:47:58.217590

Number of reads: 3285832

Percentage reads mapped: 99.57

Median coverage: 91.0

Strain: lineage1.2.2.2;lineage2.2.1;lineage3.1.2.1;lineage4

Spoligotype:

Drug-resistance: Pre-XDR-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 0.34
lineage1.2.2 Indo-Oceanic RD239 0.31
lineage3.1.2 East-African-Indian RD750 0.2
lineage2 East-Asian RD105 0.24
lineage1.2.2.2 Indo-Oceanic RD239 0.31
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.23
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
lineage4 Euro-American None 0.12
lineage1 Indo-Oceanic RD239 0.31
lineage3.1.2.1 East-African-Indian RD750 0.14
lineage3.1 East-African-Indian RD750 0.17
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 embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.15 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.37 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.23 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.13 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.36 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.16 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 0.32 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.24 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 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.49 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9163 p.Pro621Leu missense_variant 0.45 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.24 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.28 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.24 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.3 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.13 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.18 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.26 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.68 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.29 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.22 ethionamide
hadA 732110 p.Cys61Gly missense_variant 0.11 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.38 rifampicin Not assoc w R
nusG 734296 p.Asp15Asn missense_variant 0.37 rifampicin
rpoB 759746 c.-61C>T upstream_gene_variant 0.32 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 762800 c.-570C>T upstream_gene_variant 0.28 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.34 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.12 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.88 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.26 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.91 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.28 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.33 ethambutol Not assoc w R
embR 1417167 p.Glu61Lys missense_variant 0.23 ethambutol
embR 1417554 c.-207C>G upstream_gene_variant 0.28 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.32 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.24 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.94 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 0.27 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.96 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.87 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.21 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.28 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.28 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 0.25 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.38 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.43 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.36 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.23 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.25 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.41 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2752c 3064889 p.Lys435Glu missense_variant 0.26 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.1 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.27 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.27 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.32 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627602 c.-253C>T upstream_gene_variant 0.35 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3841444 c.-24G>A upstream_gene_variant 0.24 cycloserine
alr 3841546 c.-126C>A upstream_gene_variant 0.12 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.26 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.35 pyrazinamide
panD 4045162 c.-881C>T upstream_gene_variant 0.11 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.23 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 4138622 c.1134C>T synonymous_variant 0.34 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.34 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.26 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.29 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242802 c.2940G>A synonymous_variant 0.29 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.25 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.3 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.24 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.21 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.24 ethambutol Not assoc w R
aftB 4269537 c.-701G>A upstream_gene_variant 0.24 ethambutol
ubiA 4269606 c.228T>C synonymous_variant 0.33 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.35 ethionamide Uncertain significance
ethA 4328212 c.-740delC upstream_gene_variant 0.13 ethionamide
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 0.33 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338635 c.-114A>C upstream_gene_variant 0.4 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.94 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.93 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.12 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.3 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.25 streptomycin Not assoc w R
gid 4408020 c.183C>T synonymous_variant 0.33 streptomycin