TB-Profiler result

Run: ERR1633786
Summary

Run ID: ERR1633786

Sample name:

Date: 2024-04-15T00:13:01.515193

Number of reads: 2655830

Percentage reads mapped: 99.6

Median coverage: 47.0

Strain: lineage4.3.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.99
lineage4.3.2 Euro-American (LAM) None 1.0
lineage4.3.2.1 Euro-American (LAM) RD761 1.0
lineage4 Euro-American 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 katG c.-17275_*26379del Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.-1565_*43777del Assoc w R
c.-16937_*23680del Assoc w R
c.-15108_*16699del Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-38795_19del Assoc w R
c.-38257_*3783del Assoc w R
c.-34795_580del Assoc w R
c.-27543_*11737del Assoc w R
c.-22335_*8005del Assoc w R
c.-15480_*16852del Assoc w R
c.-2895_*27763del Assoc w R
c.53_*8154del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-23641_*19056del Assoc w R
c.-22383_*13719del Assoc w R
clofazimine pepQ c.-6286_*15454del Assoc w R - Interim
c.-37166_1115del Assoc w R - Interim
para-aminosalicylic_acid thyA c.-9942_*13257del Mutation from literature
c.-33681_*13005del Mutation from literature
c.-40277_*3111del Mutation from literature
c.-36986_*2800del Mutation from literature
delamanid fbiD c.-46250_*1759del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-30387_*8214del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-15606_*10263del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-2681_*38826del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-41610_*2614del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-24102_*3483del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-1417_*19417del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-27772_*10671del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-14472_*14619del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-8716_*8586del Assoc w R - Interim Confers DLM-PMD cross-resistance
bedaquiline pepQ c.-6286_*15454del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-37166_1115del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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 1879144 c.-38795_19del frameshift_variant 0.98 capreomycin Assoc w R
tlyA 1879682 c.-38257_*3783del transcript_ablation 0.97 capreomycin Assoc w R
tlyA 1883144 c.-34795_580del frameshift_variant 0.97 capreomycin Assoc w R
tlyA 1890396 c.-27543_*11737del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1895604 c.-22335_*8005del transcript_ablation 0.98 capreomycin Assoc w R
tlyA 1902459 c.-15480_*16852del transcript_ablation 0.95 capreomycin Assoc w R
tlyA 1915044 c.-2895_*27763del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1917991 c.53_*8154del frameshift_variant&stop_lost&splice_region_variant 0.96 capreomycin Assoc w R
katG 2127509 c.-17275_*26379del transcript_ablation 0.9 isoniazid Assoc w R High-level resistance
pncA 2244903 c.-1565_*43777del transcript_ablation 0.95 pyrazinamide Assoc w R
pncA 2265000 c.-16937_*23680del transcript_ablation 0.93 pyrazinamide Assoc w R
pncA 2271981 c.-15108_*16699del transcript_ablation 0.94 pyrazinamide Assoc w R
pepQ 2843845 c.-6286_*15454del transcript_ablation 0.93 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
pepQ 2859303 c.-37166_1115del frameshift_variant 0.96 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
thyA 3060422 c.-9942_*13257del transcript_ablation 0.94 para-aminosalicylic_acid Mutation from literature
thyA 3060674 c.-33681_*13005del transcript_ablation 0.93 para-aminosalicylic_acid Mutation from literature
thyA 3070568 c.-40277_*3111del transcript_ablation 0.96 para-aminosalicylic_acid Mutation from literature
thyA 3070879 c.-36986_*2800del transcript_ablation 0.93 para-aminosalicylic_acid Mutation from literature
fbiD 3292867 c.-46250_*1759del transcript_ablation 0.98 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3308730 c.-30387_*8214del transcript_ablation 0.93 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3323511 c.-15606_*10263del transcript_ablation 0.96 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3336436 c.-2681_*38826del transcript_ablation 0.96 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3598932 c.-41610_*2614del transcript_ablation 0.97 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3616440 c.-24102_*3483del transcript_ablation 0.96 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3639125 c.-1417_*19417del transcript_ablation 0.97 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3959071 c.-27772_*10671del transcript_ablation 0.96 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3972371 c.-14472_*14619del transcript_ablation 0.94 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3978127 c.-8716_*8586del transcript_ablation 0.96 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4306947 c.-23641_*19056del transcript_ablation 0.97 ethionamide Assoc w R
ethA 4312284 c.-22383_*13719del transcript_ablation 0.97 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 5520 p.Pro94Leu missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1237362 c.-17610_*15711del transcript_ablation 0.92 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1248101 c.-7759_*4972del transcript_ablation 0.97 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.98 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1829630 c.-3911_*43280del transcript_ablation 0.98 pyrazinamide Uncertain significance
rpsA 1830817 c.-2724_*5716del transcript_ablation 0.98 pyrazinamide Uncertain significance
tsnR 1836520 c.-17085_*30474del transcript_ablation 0.96 linezolid Uncertain significance
tsnR 1836636 c.-16969_*23365del transcript_ablation 0.98 linezolid Uncertain significance
tsnR 1836955 c.-16650_*2884del transcript_ablation 0.96 linezolid Uncertain significance
tsnR 1848115 c.-5490_*27854del transcript_ablation 0.97 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 2035506 c.-15190_*27302del transcript_ablation 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2045705 c.-23803_*17103del transcript_ablation 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2047182 c.-16884_*15626del transcript_ablation 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
PPE35 2164722 c.1126_*2926del stop_lost&conservative_inframe_deletion&splice_region_variant 0.97 pyrazinamide
Rv1979c 2201342 c.-3517_*20376del transcript_ablation 0.94 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290107 c.-866T>A upstream_gene_variant 1.0 pyrazinamide
kasA 2492957 c.-25157_*8426del transcript_ablation 0.94 isoniazid
eis 2696062 c.-12769_*18061del transcript_ablation 0.92 amikacin Uncertain significance
kanamycin Uncertain significance
eis 2710830 c.-8544_*3293del transcript_ablation 0.97 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2757375 c.-18464_*24990del transcript_ablation 0.93 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ribD 2951935 c.-34903_*8437del transcript_ablation 0.95 para-aminosalicylic_acid
ribD 2961956 c.-24882_*5799del transcript_ablation 0.95 para-aminosalicylic_acid
Rv2680 2965850 c.-30254_*605del transcript_ablation 0.95 capreomycin Uncertain significance
Rv2680 2984241 c.-11863_*1503del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2989311 c.-6793_*3955del transcript_ablation 0.96 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3083765 c.-3054_*25732del transcript_ablation 0.96 cycloserine
ald 3085718 c.-1101_*8107del transcript_ablation 0.93 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3420595 c.-27908_*8780del transcript_ablation 0.95 ethionamide Uncertain significance
Rv3083 3434746 c.-13757_*28950del transcript_ablation 0.93 ethionamide Uncertain significance
Rv3083 3449275 c.773_*7292del frameshift_variant&stop_lost&splice_region_variant 0.96 ethionamide Uncertain significance
Rv3083 3449736 c.1234_*38453del stop_lost&conservative_inframe_deletion&splice_region_variant 0.95 ethionamide
whiB7 3547050 c.-17131_*21350del transcript_ablation 0.97 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3565901 c.-20858_*2499del transcript_ablation 0.95 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3586579 c.-18620_*25379del transcript_ablation 0.95 pyrazinamide Uncertain significance
Rv3236c 3594447 c.-22996_*17511del transcript_ablation 0.95 pyrazinamide Uncertain significance
Rv3236c 3598517 c.-10309_*13441del transcript_ablation 0.95 pyrazinamide Uncertain significance
Rv3236c 3598621 c.-17284_*13337del transcript_ablation 0.96 pyrazinamide Uncertain significance
Rv3236c 3601012 c.-11987_*10946del transcript_ablation 0.96 pyrazinamide Uncertain significance
Rv3236c 3607818 c.50_*4140del frameshift_variant&stop_lost&splice_region_variant 0.97 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3816428 c.-5145_*23765del transcript_ablation 0.96 cycloserine
alr 3838224 c.-11802_*1969del transcript_ablation 0.96 cycloserine
rpoA 3848185 c.-16826_*29278del transcript_ablation 0.96 rifampicin
rpoA 3868362 c.-38781_*9101del transcript_ablation 0.98 rifampicin
rpoA 3873538 c.-43756_*3925del transcript_ablation 0.98 rifampicin
clpC1 4014460 c.-681_*23697del transcript_ablation 0.95 pyrazinamide
panD 4017822 c.-21679_*26039del transcript_ablation 0.94 pyrazinamide Uncertain significance
panD 4026791 c.-25199_*17070del transcript_ablation 0.95 pyrazinamide Uncertain significance
panD 4034108 c.-11110_*9753del transcript_ablation 0.95 pyrazinamide Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
glpK 4102251 c.-7482_*35950del transcript_ablation 0.97 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4102779 c.942_*35422del frameshift_variant&stop_lost&splice_region_variant 0.96 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4103269 c.-1920_*34932del transcript_ablation 0.96 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4113112 c.-9885_*25089del transcript_ablation 0.97 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4113972 c.326_*24229del frameshift_variant&stop_lost&splice_region_variant 0.98 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embA 4229854 c.-13378_*453del transcript_ablation 0.95 ethambutol Uncertain significance
embA 4234112 c.-9120_*27554del transcript_ablation 0.97 ethambutol Uncertain significance
embA 4240504 c.-2728_*21302del transcript_ablation 0.98 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268296 c.-24979_540del start_lost&conservative_inframe_deletion 0.96 ethambutol Uncertain significance
whiB6 4338145 c.-29795_*25del transcript_ablation 0.97 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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R