TB-Profiler result

Run: SAMN02414843
Summary

Run ID: SAMN02414843

Sample name:

Date: 2024-10-05T02:09:30.084324

Number of reads: 20812035

Percentage reads mapped: 98.82

Median coverage: 410.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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.Ala286Val Uncertain significance Mutation from literature
p.Ser450Leu Assoc w R
isoniazid katG c.-7898_*21866del Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.-14157_*7700del Assoc w R
streptomycin gid c.-306_*28299del Assoc w R
c.-861_*16579del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.627_*44375del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-25870_*21066del Assoc w R
c.-25838_*14482del Assoc w R
c.-19687_*1475del Assoc w R
c.-40368_*1333del Assoc w R
clofazimine pepQ c.-12959_*20053del Assoc w R - Interim
c.-4830_*16381del Assoc w R - Interim
c.-7764_*15122del Assoc w R - Interim
para-aminosalicylic_acid thyA c.-28320_*6105del Mutation from literature
delamanid fbiD c.-25630_*5104del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-18518_*15625del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-1873_*38786del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-32884_*14581del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-16708_*10917del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-15577_*15250del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-11453_*4741del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-10403_*33162del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-4678_*32853del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-284_*36132del Assoc w R - Interim Confers DLM-PMD cross-resistance
bedaquiline pepQ c.-12959_*20053del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-4830_*16381del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-7764_*15122del 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
rpoB 760663 p.Ala286Val missense_variant 0.99 rifampicin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
tlyA 1918565 c.627_*44375del frameshift_variant&stop_lost&splice_region_variant 0.93 capreomycin Assoc w R
katG 2132022 c.-7898_*21866del transcript_ablation 0.9 isoniazid Assoc w R High-level resistance
pncA 2280980 c.-14157_*7700del transcript_ablation 0.9 pyrazinamide Assoc w R
pepQ 2839246 c.-12959_*20053del transcript_ablation 0.94 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 2842918 c.-4830_*16381del transcript_ablation 0.94 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 2844177 c.-7764_*15122del transcript_ablation 0.91 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 3067574 c.-28320_*6105del transcript_ablation 0.94 para-aminosalicylic_acid Mutation from literature
fbiD 3313487 c.-25630_*5104del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3320599 c.-18518_*15625del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3638669 c.-1873_*38786del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3953959 c.-32884_*14581del transcript_ablation 0.93 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3970135 c.-16708_*10917del 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 3971266 c.-15577_*15250del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3975390 c.-11453_*4741del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3976440 c.-10403_*33162del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3982165 c.-4678_*32853del transcript_ablation 0.93 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3986559 c.-284_*36132del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4304937 c.-25870_*21066del transcript_ablation 0.93 ethionamide Assoc w R
ethA 4311521 c.-25838_*14482del transcript_ablation 0.94 ethionamide Assoc w R
ethA 4324528 c.-19687_*1475del transcript_ablation 0.91 ethionamide Assoc w R
ethA 4324670 c.-40368_*1333del transcript_ablation 0.92 ethionamide Assoc w R
gid 4379228 c.-306_*28299del transcript_ablation 0.94 streptomycin Assoc w R
gid 4390948 c.-861_*16579del transcript_ablation 0.93 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 1.0 ethionamide Uncertain significance
Rv0565c 656636 p.Gly279Cys missense_variant 1.0 ethionamide
nusG 734658 c.405A>G synonymous_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
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 1652627 c.-21574_*8462del transcript_ablation 0.92 isoniazid
ethionamide
rpsA 1800105 c.-33436_*11603del transcript_ablation 0.91 pyrazinamide Uncertain significance
tsnR 1846428 c.-7177_*34310del transcript_ablation 0.93 linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2045138 c.-23360_*17670del transcript_ablation 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
PPE35 2168149 p.Pro822Ser missense_variant 0.99 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2471869 c.-46245_1073del exon_loss_variant 0.92 isoniazid
kasA 2498225 c.-19889_*17093del transcript_ablation 0.9 isoniazid
eis 2705775 c.-22020_*8348del transcript_ablation 0.92 kanamycin Uncertain significance
amikacin Uncertain significance
eis 2712823 c.-26786_*1300del transcript_ablation 0.93 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2715790 c.-10402_*2600del transcript_ablation 0.91 isoniazid Uncertain significance
Rv2477c 2774436 c.-25472_*7929del transcript_ablation 0.9 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2680 2960952 c.-35152_*2431del transcript_ablation 0.97 capreomycin Uncertain significance
Rv2680 2960973 c.-35131_*11438del transcript_ablation 0.92 capreomycin Uncertain significance
Rv2680 2961355 c.-34749_*14125del transcript_ablation 0.93 capreomycin Uncertain significance
Rv2680 2987844 c.-8260_*822del transcript_ablation 0.92 capreomycin Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.99 capreomycin
Rv3083 3427072 c.-21431_*24962del transcript_ablation 0.95 ethionamide Uncertain significance
Rv3083 3428565 c.-19938_*13117del transcript_ablation 0.93 ethionamide Uncertain significance
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0 ethionamide
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
Rv3236c 3576097 c.872_*35861del frameshift_variant&stop_lost&splice_region_variant 0.92 pyrazinamide Uncertain significance
Rv3236c 3583506 c.-2297_*28452del transcript_ablation 0.91 pyrazinamide Uncertain significance
Rv3236c 3586453 c.745_*25505del stop_lost&conservative_inframe_deletion&splice_region_variant 0.92 pyrazinamide
Rv3236c 3596803 c.-19308_*15155del transcript_ablation 0.9 pyrazinamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 1.0 pyrazinamide Not assoc w R
alr 3804090 c.-2985_*36103del transcript_ablation 0.93 cycloserine
alr 3815199 c.-23219_*24994del transcript_ablation 0.96 cycloserine
alr 3819171 c.-22390_*21022del transcript_ablation 0.95 cycloserine
alr 3830450 c.-16796_*9743del transcript_ablation 0.93 cycloserine
alr 3834117 c.-31992_*6076del transcript_ablation 0.93 cycloserine
rpoA 3852537 c.-16507_*24926del transcript_ablation 0.92 rifampicin
rpoA 3860251 c.-22270_*17212del transcript_ablation 0.93 rifampicin
rpoA 3867530 c.-21139_*9933del transcript_ablation 0.91 rifampicin
rpoA 3870610 c.-34241_*6853del transcript_ablation 0.91 rifampicin
rpoA 3870800 c.-25784_*6663del transcript_ablation 0.91 rifampicin
rpoA 3871205 c.-39355_*6258del transcript_ablation 0.92 rifampicin
panD 4016091 c.-19913_*27770del transcript_ablation 0.95 pyrazinamide Uncertain significance
panD 4021751 c.-12898_*22110del transcript_ablation 0.91 pyrazinamide Uncertain significance
panD 4038215 c.-25039_*5646del transcript_ablation 0.93 pyrazinamide Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 1.0 pyrazinamide Not assoc w R
glpK 4114198 c.-6508_*24003del transcript_ablation 0.92 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4130416 c.-10897_*7785del transcript_ablation 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4135558 c.-5783_*2643del transcript_ablation 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embA 4203031 c.-40201_*1494del transcript_ablation 0.93 ethambutol Uncertain significance
embC 4211482 c.-28380_2792del frameshift_variant&start_lost 0.9 ethambutol
embA 4218293 c.-24939_*21214del transcript_ablation 0.92 ethambutol Uncertain significance
embA 4227075 c.-16157_*27835del transcript_ablation 0.9 ethambutol Uncertain significance
embA 4233247 c.-9985_*23753del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4238016 c.-5216_*1009del transcript_ablation 0.92 ethambutol Uncertain significance
embC 4238407 c.-1455_1053del start_lost&conservative_inframe_deletion 0.91 ethambutol
embC 4239361 c.-501_*1432del transcript_ablation 0.96 ethambutol
embC 4240549 c.688_3020del frameshift_variant 0.92 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4244531 c.-3143_*22421del transcript_ablation 0.91 ethambutol Uncertain significance
embA 4244847 c.1616_*1100del frameshift_variant&stop_lost&splice_region_variant 0.95 ethambutol Uncertain significance
embB 4246695 c.183_*10239del frameshift_variant&stop_lost&splice_region_variant 0.95 ethambutol
aftB 4268508 c.-41356_328del frameshift_variant&start_lost 0.92 ethambutol Uncertain significance
whiB6 4331855 c.-32601_*6315del transcript_ablation 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338593 c.-73delT upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin