TB-Profiler result

Run: SAMN02231179
Summary

Run ID: SAMN02231179

Sample name:

Date: 2024-04-15T22:04:22.217293

Number of reads: 14338417

Percentage reads mapped: 98.01

Median coverage: 282.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.99
lineage4.1 Euro-American None 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 rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG c.-8137_*1469del Assoc w R High-level resistance
p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Pro54Leu Assoc w R
streptomycin gid c.-970_*46024del Assoc w R
c.-1810_*39433del Assoc w R
p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.-24907_*22804del Assoc w R
c.-19477_*14436del Assoc w R
c.-19305_*6538del Assoc w R
c.-25853_*5595del Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid fbiA c.-40495_*5945del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-11425_*32392del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-32364_*10373del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-32360_*15783del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-18495_*18954del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-15682_*25301del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-12258_*36842del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-8933_*15239del 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.96 isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
katG 2152419 c.-8137_*1469del transcript_ablation 0.9 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2289081 p.Pro54Leu missense_variant 0.99 pyrazinamide Assoc w R
fbiA 3600047 c.-40495_*5945del transcript_ablation 0.92 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3629117 c.-11425_*32392del transcript_ablation 0.91 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3954479 c.-32364_*10373del transcript_ablation 0.9 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3954483 c.-32360_*15783del transcript_ablation 0.9 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3968348 c.-18495_*18954del transcript_ablation 0.91 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3971161 c.-15682_*25301del 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 3974585 c.-12258_*36842del transcript_ablation 0.9 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3977910 c.-8933_*15239del transcript_ablation 0.9 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol Assoc w R
ethA 4303199 c.-24907_*22804del transcript_ablation 0.92 ethionamide Assoc w R
ethA 4311567 c.-19477_*14436del transcript_ablation 0.91 ethionamide Assoc w R
ethA 4319465 c.-19305_*6538del transcript_ablation 0.92 ethionamide Assoc w R
ethA 4320408 c.-25853_*5595del transcript_ablation 0.93 ethionamide Assoc w R
gid 4361503 c.-970_*46024del transcript_ablation 0.91 streptomycin Assoc w R
gid 4368094 c.-1810_*39433del transcript_ablation 0.91 streptomycin Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.98 streptomycin Uncertain significance Mutation from literature
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
gyrA 9557 c.2256G>C synonymous_variant 0.96 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.99 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 0.99 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1129c 1254327 p.Asp70Asn missense_variant 0.97 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1304610 c.1680C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
PPE35 2165090 c.1290_*2558del frameshift_variant&stop_lost&splice_region_variant 0.91 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3535042 c.-979_*33358del transcript_ablation 0.9 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3588968 c.-3056_*22990del transcript_ablation 0.91 pyrazinamide Uncertain significance
Rv3236c 3597851 c.-2673_*14107del transcript_ablation 0.91 pyrazinamide Uncertain significance
Rv3236c 3611500 c.-17311_*458del transcript_ablation 0.9 pyrazinamide Uncertain significance
lpqB 3616305 c.-10559_*6853del transcript_ablation 0.9 bedaquiline
rifampicin Uncertain significance
lpqB 3623291 c.1620C>A synonymous_variant 0.97 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624660 p.Ala84Gly missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3854479 c.30_*22984del frameshift_variant&stop_lost&splice_region_variant 0.9 rifampicin
glpK 4114430 c.-9694_*23771del transcript_ablation 0.91 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4121927 c.-9060_*16274del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4126422 c.-22887_*11779del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4130829 c.-34640_*7372del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4130925 c.-12727_*7276del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4132915 c.-18144_*5286del transcript_ablation 0.91 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4136195 c.-8238_*2006del transcript_ablation 0.92 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4136728 c.-32907_*1473del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4136748 c.-18432_*1453del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.97 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embA 4200898 c.-42334_823del frameshift_variant 0.92 ethambutol Uncertain significance
embA 4210401 c.-32831_*2890del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4213041 c.-30191_*1379del transcript_ablation 0.9 ethambutol Uncertain significance
embA 4220553 c.-22679_*187del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4227833 c.-15399_*31278del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4238584 c.-4648_*1833del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4239514 c.-3718_*41354del transcript_ablation 0.91 ethambutol Uncertain significance
embC 4239531 c.-331_3003del start_lost&conservative_inframe_deletion 0.91 ethambutol
embA 4239720 c.-3512_*21836del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4239935 c.-3297_*29415del transcript_ablation 0.91 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4243286 c.-3227_*2051del transcript_ablation 0.9 ethambutol
embA 4244529 c.1298_*859del frameshift_variant&stop_lost&splice_region_variant 0.91 ethambutol Uncertain significance
aftB 4249511 c.-30427_*17441del transcript_ablation 0.9 ethambutol Uncertain significance
aftB 4256479 c.-9665_*10473del transcript_ablation 0.9 ethambutol Uncertain significance
aftB 4266843 c.-15134_*109del transcript_ablation 0.92 ethambutol Uncertain significance
aftB 4267740 c.-31364_1096del frameshift_variant&start_lost 0.91 ethambutol Uncertain significance
aftB 4268167 c.-27104_669del start_lost&conservative_inframe_deletion 0.91 ethambutol Uncertain significance
ubiA 4269311 p.Trp175Arg missense_variant 0.98 ethambutol Uncertain significance
ubiA 4269444 c.-45313_389del exon_loss_variant 0.91 ethambutol
whiB6 4328323 c.-38548_*9847del transcript_ablation 0.9 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4330819 c.-27918_*7351del transcript_ablation 0.92 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4331441 c.-13873_*6729del transcript_ablation 0.93 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