TB-Profiler result

Run: ERR8975003
Summary

Run ID: ERR8975003

Sample name:

Date: 2024-10-04T09:28:14.853293

Number of reads: 2799795

Percentage reads mapped: 99.66

Median coverage: 90.0

Strain: lineage2.2.1;lineage4.4.1.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1.1.1 Euro-American None 0.15
lineage2 East-Asian RD105 0.85
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.83
lineage2.2 East-Asian (Beijing) RD105;RD207 0.85
lineage4.4.1 Euro-American (S-type) None 0.15
lineage4 Euro-American None 0.16
lineage4.4.1.1 Euro-American None 0.19
lineage4.4 Euro-American None 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 pncA p.Tyr34Asp Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
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 0.16 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.84 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 0.14 isoniazid Assoc w R High-level resistance
pncA 2289142 p.Tyr34Asp missense_variant 0.2 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.19 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.75 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.85 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.83 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.82 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.86 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Ser missense_variant 0.19 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 0.92 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.88 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.94 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833254 c.-288G>C upstream_gene_variant 0.78 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.84 pyrazinamide Not assoc w R - Interim
tsnR 1853674 c.69G>A synonymous_variant 0.14 linezolid Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.19 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.83 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.28 pyrazinamide 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.13 para-aminosalicylic_acid
Rv2752c 3064993 p.Trp400* stop_gained 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339117 c.-1C>A upstream_gene_variant 0.85 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiD 3339287 p.Arg57Leu missense_variant 0.11 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.28 ethionamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.8 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641332 p.Gly264Arg missense_variant 0.78 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.18 ethambutol Not assoc w R
embC 4239274 c.-589C>G upstream_gene_variant 0.18 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 0.84 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.94 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.88 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.77 streptomycin Not assoc w R