TB-Profiler result

Run: ERR495192
Summary

Run ID: ERR495192

Sample name:

Date: 2024-10-03T15:44:36.488295

Number of reads: 3470628

Percentage reads mapped: 99.07

Median coverage: 66.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.1 Euro-American (X-type) RD183 0.9
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-38692_*9219del Assoc w R
c.-31231_*9077del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-19340_*15714del Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid ddn c.-29525_*10761del Assoc w R - Interim Confers DLM-PMD cross-resistance
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
tlyA 1879247 c.-38692_*9219del transcript_ablation 0.95 capreomycin Assoc w R
tlyA 1886708 c.-31231_*9077del transcript_ablation 0.93 capreomycin Assoc w R
ddn 3957318 c.-29525_*10761del transcript_ablation 0.93 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4310289 c.-19340_*15714del transcript_ablation 0.92 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
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
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1835389 c.-18216_*24824del transcript_ablation 0.91 linezolid Uncertain significance
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
bacA 2046294 c.-23668_*16514del transcript_ablation 0.91 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
PPE35 2164652 c.1295_*2996del frameshift_variant&stop_lost&splice_region_variant 0.94 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726210 c.18T>C synonymous_variant 0.98 isoniazid Not assoc w R - Interim
Rv2680 2976205 c.-19899_*7340del transcript_ablation 0.9 capreomycin Uncertain significance
Rv2680 2980122 c.-15982_*32439del transcript_ablation 0.91 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087857 c.1038C>T synonymous_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641447 p.Thr302Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
alr 3841006 p.Asp139Asn missense_variant 1.0 cycloserine
rpoA 3873264 c.-13656_*4199del transcript_ablation 0.93 rifampicin
rpoA 3877553 p.Glu319Lys missense_variant 1.0 rifampicin Not assoc w R
glpK 4111779 c.-10820_*26422del transcript_ablation 0.92 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240897 c.1035C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.29 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.33 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.26 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.23 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338498 p.Glu8Asp missense_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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