TB-Profiler result

Run: ERR1633942
Summary

Run ID: ERR1633942

Sample name:

Date: 2024-10-05T13:48:35.300220

Number of reads: 2256141

Percentage reads mapped: 99.58

Median coverage: 40.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.99
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.-24753_*21349del Assoc w R High-level resistance
c.-18218_*20165del Assoc w R High-level resistance
c.-7448_*20004del Assoc w R High-level resistance
c.-8869_*11120del Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.-8144_*32576del Assoc w R
c.-6658_*24718del Assoc w R
c.-23131_*13371del Assoc w R
streptomycin gid c.-831_*46455del Assoc w R
c.-317_*15691del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-31753_*9471del Assoc w R
c.-27967_*16974del Assoc w R
c.-27644_*8562del Assoc w R
c.-19279_*6306del Assoc w R
c.-11399_*433del Assoc w R
c.651_*9270del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-25881_*18417del Assoc w R
c.-29195_*10380del Assoc w R
c.-29466_*4461del Assoc w R
c.-24669_*555del Assoc w R
clofazimine pepQ c.-20764_*28010del Assoc w R - Interim
c.629_*16192del Assoc w R - Interim
c.-29339_*3619del Assoc w R - Interim
para-aminosalicylic_acid thyA c.-2591_*21377del Mutation from literature
c.-31013_*12637del Mutation from literature
delamanid fgd1 c.-36865_*3868del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-2815_*38227del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiC c.-8681_*28067del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-254_*42804del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD c.-38231_*6384del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-14926_15del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-13645_*15277del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-6876_*39165del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-40167_*5880del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-27298_*14797del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-24858_*3793del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-16524_*11937del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-3998_*16876del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-16771_*11487del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-8691_*22771del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-3952_*18693del Assoc w R - Interim Confers DLM-PMD cross-resistance
bedaquiline pepQ c.-20764_*28010del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.629_*16192del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-29339_*3619del 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
fgd1 453917 c.-36865_*3868del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fgd1 487967 c.-2815_*38227del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiC 1294249 c.-8681_*28067del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiC 1302676 c.-254_*42804del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
tlyA 1886186 c.-31753_*9471del transcript_ablation 0.96 capreomycin Assoc w R
tlyA 1889972 c.-27967_*16974del transcript_ablation 0.95 capreomycin Assoc w R
tlyA 1890295 c.-27644_*8562del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1898660 c.-19279_*6306del transcript_ablation 0.98 capreomycin Assoc w R
tlyA 1906540 c.-11399_*433del transcript_ablation 0.92 capreomycin Assoc w R
tlyA 1918589 c.651_*9270del frameshift_variant&stop_lost&splice_region_variant 0.96 capreomycin Assoc w R
katG 2132539 c.-24753_*21349del transcript_ablation 0.92 isoniazid Assoc w R High-level resistance
katG 2133723 c.-18218_*20165del transcript_ablation 0.93 isoniazid Assoc w R High-level resistance
katG 2133884 c.-7448_*20004del transcript_ablation 0.98 isoniazid Assoc w R High-level resistance
katG 2142768 c.-8869_*11120del transcript_ablation 0.97 isoniazid Assoc w R High-level resistance
pncA 2256104 c.-8144_*32576del transcript_ablation 0.96 pyrazinamide Assoc w R
pncA 2263962 c.-6658_*24718del transcript_ablation 0.94 pyrazinamide Assoc w R
pncA 2275309 c.-23131_*13371del transcript_ablation 0.95 pyrazinamide Assoc w R
pepQ 2831289 c.-20764_*28010del transcript_ablation 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
pepQ 2843107 c.629_*16192del frameshift_variant&stop_lost&splice_region_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
pepQ 2855680 c.-29339_*3619del transcript_ablation 0.97 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 3052302 c.-2591_*21377del transcript_ablation 0.97 para-aminosalicylic_acid Mutation from literature
thyA 3061042 c.-31013_*12637del transcript_ablation 0.97 para-aminosalicylic_acid Mutation from literature
fbiD 3300886 c.-38231_*6384del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3324191 c.-14926_15del start_lost&conservative_inframe_deletion 0.96 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3325472 c.-13645_*15277del transcript_ablation 0.99 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3332241 c.-6876_*39165del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3600375 c.-40167_*5880del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3613244 c.-27298_*14797del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3615684 c.-24858_*3793del transcript_ablation 0.96 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3624018 c.-16524_*11937del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3636544 c.-3998_*16876del transcript_ablation 0.98 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3970072 c.-16771_*11487del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3978152 c.-8691_*22771del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3982891 c.-3952_*18693del transcript_ablation 0.97 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4307586 c.-25881_*18417del transcript_ablation 0.99 ethionamide Assoc w R
ethA 4315623 c.-29195_*10380del transcript_ablation 0.98 ethionamide Assoc w R
ethA 4321542 c.-29466_*4461del transcript_ablation 0.96 ethionamide Assoc w R
ethA 4325448 c.-24669_*555del transcript_ablation 0.98 ethionamide Assoc w R
gid 4361072 c.-831_*46455del transcript_ablation 0.96 streptomycin Assoc w R
gid 4391836 c.-317_*15691del transcript_ablation 0.99 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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 532647 c.-42700_*1327del transcript_ablation 0.92 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 622638 c.-8250_*33371del transcript_ablation 0.91 ethionamide Uncertain significance
hadA 723568 c.-8361_*17662del transcript_ablation 0.92 isoniazid Uncertain significance
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 799178 c.-1630_*44673del transcript_ablation 0.96 linezolid
Rv1129c 1239196 c.-33920_*13877del transcript_ablation 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1242541 c.-6923_*10532del transcript_ablation 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1252531 c.-20791_*542del transcript_ablation 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
sigE 1336297 c.-28115_*14620del transcript_ablation 0.93 pyrazinamide Uncertain significance
sigE 1364409 c.-3_*44962del transcript_ablation 0.92 pyrazinamide Uncertain significance
Rv1258c 1400026 c.-28446_*6054del transcript_ablation 0.95 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
atpE 1451259 c.-9785_145del frameshift_variant&start_lost 0.93 bedaquiline
atpE 1460336 c.-708_*6415del transcript_ablation 0.92 bedaquiline
rrs 1461935 n.-9910_*21776del transcript_ablation 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1640481 c.-33720_*9715del transcript_ablation 0.97 isoniazid
ethionamide
inhA 1663359 c.-10842_*9988del transcript_ablation 0.94 isoniazid
ethionamide
rpsA 1791942 c.-41599_*3775del transcript_ablation 0.97 pyrazinamide Uncertain significance
rpsA 1823476 c.-10065_*10454del transcript_ablation 0.93 pyrazinamide Uncertain significance
rpsA 1830930 c.-2611_*39607del transcript_ablation 0.96 pyrazinamide Uncertain significance
tsnR 1839758 c.-13847_*23969del transcript_ablation 0.97 linezolid Uncertain significance
tsnR 1840144 c.-13461_*30539del transcript_ablation 0.97 linezolid Uncertain significance
tsnR 1844842 c.-8763_*22317del transcript_ablation 0.98 linezolid Uncertain significance
tsnR 1844933 c.-8672_*15538del transcript_ablation 0.96 linezolid Uncertain significance
tsnR 1851474 c.-2131_*31558del transcript_ablation 0.96 linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918287 c.349_*20213del stop_lost&conservative_inframe_deletion&splice_region_variant 0.95 capreomycin
bacA 2019261 c.-1778_*43547del transcript_ablation 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
bacA 2024008 c.-4846_*38800del transcript_ablation 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
bacA 2039601 c.-12688_*23207del transcript_ablation 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
bacA 2045808 c.-23554_*17000del transcript_ablation 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
bacA 2051553 c.-24738_*11255del transcript_ablation 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
bacA 2056692 c.1354_*6116del stop_lost&conservative_inframe_deletion&splice_region_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
ndh 2081655 c.-9374_*19995del transcript_ablation 0.97 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
ndh 2098729 c.-32661_*2921del transcript_ablation 0.96 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
ndh 2102141 c.-46953_901del frameshift_variant&start_lost 0.96 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
Rv1979c 2209213 c.-226_*12505del transcript_ablation 0.95 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2209736 c.-35832_*11982del transcript_ablation 0.96 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2213300 c.-22678_*8418del transcript_ablation 0.92 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2217972 c.-43112_*3746del transcript_ablation 0.95 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2219568 c.-19174_*2150del transcript_ablation 0.95 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
kasA 2502673 c.-15441_*13192del transcript_ablation 0.97 isoniazid
eis 2696566 c.-30371_*17557del transcript_ablation 0.96 kanamycin Uncertain significance
amikacin Uncertain significance
eis 2697690 c.-6730_*16433del transcript_ablation 0.96 kanamycin Uncertain significance
amikacin Uncertain significance
eis 2706951 c.-30483_*7172del transcript_ablation 0.96 kanamycin Uncertain significance
amikacin Uncertain significance
eis 2707788 c.-6274_*6335del transcript_ablation 0.94 kanamycin Uncertain significance
amikacin Uncertain significance
folC 2733223 c.263_*12911del frameshift_variant&stop_lost&splice_region_variant 0.96 para-aminosalicylic_acid
folC 2745882 c.-9464_*252del transcript_ablation 0.95 para-aminosalicylic_acid
Rv2477c 2757738 c.-20274_*24627del transcript_ablation 0.95 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2771646 c.-22590_*10719del transcript_ablation 0.96 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2775830 c.-30233_*6535del transcript_ablation 0.98 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
ribD 2963172 c.-23666_*5280del transcript_ablation 0.97 para-aminosalicylic_acid
Rv2680 2995745 c.-359_*43052del transcript_ablation 0.97 capreomycin Uncertain significance
ald 3077531 c.-9288_*14247del transcript_ablation 0.94 cycloserine
ald 3086384 c.-435_*40785del transcript_ablation 0.96 cycloserine
whiB7 3561248 c.-23521_*7152del transcript_ablation 0.97 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3579533 c.-3626_*32425del transcript_ablation 0.97 pyrazinamide Uncertain significance
fbiB 3642491 c.958_*20821del stop_lost&conservative_inframe_deletion&splice_region_variant 0.96 pretomanid
delamanid
clofazimine
alr 3837416 c.-20207_*2777del transcript_ablation 0.96 cycloserine
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
rpoA 3858465 c.-15041_*18998del transcript_ablation 0.95 rifampicin
rpoA 3869014 c.-25608_*8449del transcript_ablation 0.97 rifampicin
panD 4015602 c.-20906_*28259del transcript_ablation 0.98 pyrazinamide Uncertain significance
glpK 4105225 c.-10781_*32976del transcript_ablation 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4112833 c.-11508_*25368del transcript_ablation 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4113665 c.-3543_*24536del transcript_ablation 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4124415 c.-24232_*13786del transcript_ablation 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4135837 c.-22512_*2364del transcript_ablation 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4138130 c.-14050_*71del transcript_ablation 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embA 4223733 c.-19499_*20841del transcript_ablation 0.97 ethambutol Uncertain significance
embA 4237111 c.-6121_*9932del transcript_ablation 0.97 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4258897 c.1095_*8055del frameshift_variant&stop_lost&splice_region_variant 0.98 ethambutol Uncertain significance
aftB 4268254 c.-46053_582del start_lost&conservative_inframe_deletion 0.98 ethambutol Uncertain significance
ubiA 4269034 c.-33460_799del frameshift_variant&start_lost 0.98 ethambutol
ethA 4328419 c.-946G>A upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R