TB-Profiler result

Run: SRR16156738
Summary

Run ID: SRR16156738

Sample name:

Date: 2024-10-04T15:19:45.957085

Number of reads: 1645799

Percentage reads mapped: 99.6

Median coverage: 54.0

Strain: lineage2.2.1.1;lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.79
lineage4.1 Euro-American None 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.81
lineage4.1.1.3 Euro-American (X-type) RD193 0.18
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 0.21
lineage4.1.1 Euro-American (X-type) None 0.18
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.82
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
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg 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
ethA c.597delC Assoc w R
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 0.35 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.25 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.81 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.79 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 2155167 p.Ser315Thr missense_variant 0.21 isoniazid Assoc w R High-level resistance
ahpC 2726145 c.-48G>A upstream_gene_variant 0.2 isoniazid Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.12 ethambutol Assoc w R
ethA 4326876 c.597delC frameshift_variant 0.19 ethionamide 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 6608 p.Val457Leu missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.82 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 0.9 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.85 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.84 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.7 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.3 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.23 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 0.88 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.86 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 0.73 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.12 linezolid
rplC 801354 c.546G>A synonymous_variant 0.19 linezolid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.82 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 0.75 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.73 pyrazinamide 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 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.86 pyrazinamide Not assoc w R
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.7 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288901 p.Thr114Met missense_variant 0.82 pyrazinamide Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.8 kanamycin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449616 p.Met371Ile missense_variant 0.21 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75 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 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.8 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.73 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.27 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.72 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 0.85 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.87 streptomycin Not assoc w R