TB-Profiler result

Run: SRR921503
Summary

Run ID: SRR921503

Sample name:

Date: 2024-10-04T21:07:59.684288

Number of reads: 6087573

Percentage reads mapped: 99.35

Median coverage: 112.0

Strain: lineage2.2.1;lineage4.4.2

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
lineage2 East-Asian RD105 0.14
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.15
lineage2.2 East-Asian (Beijing) RD105;RD207 0.15
lineage4 Euro-American None 0.84
lineage4.4 Euro-American None 0.86
lineage4.4.2 Euro-American None 0.86
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.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG c.1670delA Assoc w R High-level resistance
p.Ser315Asn Assoc w R High-level resistance
ethambutol embA c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Cys72Tyr Assoc w R - Interim
streptomycin rrs n.514A>C Assoc w R
gid p.Lys163* 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 rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.1021_1022dupGC Assoc w R
clofazimine
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
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 0.83 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.1 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.11 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.14 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2154441 c.1670delA frameshift_variant 0.14 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Asn missense_variant 0.88 isoniazid Assoc w R High-level resistance
pncA 2289027 p.Cys72Tyr missense_variant 0.17 pyrazinamide Assoc w R - Interim
thyA 3074408 p.Thr22Ala missense_variant 0.18 para-aminosalicylic_acid Mutation from literature
embA 4243222 c.-11C>A upstream_gene_variant 0.84 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.13 ethambutol Assoc w R
ethA 4326451 c.1021_1022dupGC frameshift_variant 0.16 ethionamide Assoc w R
gid 4407716 p.Lys163* stop_gained 0.89 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
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 491556 c.774G>A synonymous_variant 0.13 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.12 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575503 c.156G>A synonymous_variant 0.81 isoniazid Not assoc w R - Interim
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656246 c.1224dupA frameshift_variant 0.22 ethionamide Uncertain significance
Rv0565c 656317 p.Phe385Ser missense_variant 0.48 ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.18 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.21 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 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.14 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.15 bedaquiline
clofazimine
rpsL 781326 c.-233delG upstream_gene_variant 0.84 streptomycin Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674210 c.9A>C synonymous_variant 0.18 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
rpsA 1833491 c.-51A>G upstream_gene_variant 0.14 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.1 pyrazinamide Not assoc w R - Interim
tsnR 1853445 c.-161G>C upstream_gene_variant 0.79 linezolid
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
ndh 2102365 c.678A>C synonymous_variant 0.89 isoniazid Not assoc w R - Interim
delamanid
ethionamide
ndh 2102465 p.Ala193Asp missense_variant 0.11 isoniazid Uncertain significance
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid Not assoc w R
katG 2156484 c.-373A>G upstream_gene_variant 0.8 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.16 pyrazinamide Not assoc w R
PPE35 2169411 c.1201dupA frameshift_variant 0.81 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289538 c.-297G>A upstream_gene_variant 0.13 pyrazinamide
Rv2752c 3066099 p.Met31Ile missense_variant 0.9 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625342 c.1272C>G synonymous_variant 0.84 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
embC 4238963 c.-900C>T upstream_gene_variant 0.88 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244329 p.Ala366Glu missense_variant 0.77 ethambutol
embA 4246508 c.3276G>A synonymous_variant 0.81 ethambutol Not assoc w R
embB 4248026 p.Ala505Thr missense_variant 0.58 ethambutol Uncertain significance
aftB 4267512 p.Leu442His missense_variant 0.86 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.17 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.89 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.86 ethambutol Not assoc w R
ethA 4326977 p.His166Pro missense_variant 0.85 ethionamide Uncertain significance
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 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.12 streptomycin Not assoc w R