TB-Profiler result

Run: SRR25827775

Summary

Run ID: SRR25827775

Sample name:

Date: 2024-04-14T13:47:21.972407

Number of reads: 5999602

Percentage reads mapped: 99.03

Median coverage: 204.0

Strain: lineage2.2.1;lineage3

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 0.44
lineage2 East-Asian RD105 0.53
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.56
lineage2.2 East-Asian (Beijing) RD105;RD207 0.56
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.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. 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 c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
clofazimine
para-aminosalicylic_acid folC p.Ile43Thr 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
rpoB 761155 p.Ser450Leu missense_variant 0.53 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.52 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.71 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
inhA 1673432 c.-770T>A upstream_gene_variant 0.55 isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
katG 2155168 p.Ser315Thr missense_variant 0.55 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.52 pyrazinamide Assoc w R
folC 2747471 p.Ile43Thr missense_variant 0.56 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.52 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 8164 p.Ala288Asp missense_variant 0.55 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9128 c.1827C>A synonymous_variant 0.5 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.58 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.55 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.52 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.4 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 767123 p.Val1252Leu missense_variant 0.61 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 0.58 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.56 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 2154242 p.Met624Val missense_variant 0.54 isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289365 c.-125delC upstream_gene_variant 0.51 pyrazinamide
eis 2714629 p.Leu235Arg missense_variant 0.55 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 0.51 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.42 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.52 streptomycin
amikacin
kanamycin
Rv3236c 3612418 c.699C>T synonymous_variant 0.46 pyrazinamide Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.53 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642877 p.Lys448Arg missense_variant 0.46 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.46 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.48 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
glpK 4139246 c.510C>T synonymous_variant 0.44 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.47 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 0.48 ethambutol Not assoc w R
embA 4244657 c.1425G>A synonymous_variant 0.48 ethambutol
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
embB 4248353 p.Val614Ile missense_variant 0.53 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.48 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.6 ethionamide Uncertain significance
ethA 4327344 p.Thr44Ala missense_variant 0.46 ethionamide Uncertain significance
whiB6 4338266 p.Arg86Trp missense_variant 0.55 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.52 streptomycin Not assoc w R