TB-Profiler result

Run: ERR279638
Summary

Run ID: ERR279638

Sample name:

Date: 2024-04-16T08:16:49.765752

Number of reads: 3397225

Percentage reads mapped: 99.53

Median coverage: 61.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

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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
ethambutol
pyrazinamide pncA c.-13885_*27155del Assoc w R
c.-27535_*21094del Assoc w R
c.-8342_*20800del Assoc w R
streptomycin gid c.-2365_*16430del Assoc w R
c.150_*6245del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-37690_*7765del Assoc w R
c.-36646_*331del Assoc w R
c.-27465_*9198del Assoc w R
c.-20192_*4058del Assoc w R
c.-14630_*27615del Assoc w R
c.-13002_*7098del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-12201_*17058del Assoc w R
c.-26066_*15674del Assoc w R
c.372_*12531del Assoc w R
c.-18092_*6426del Assoc w R
c.-2103_*5979del Assoc w R
clofazimine pepQ c.-9597_*35883del Assoc w R - Interim
c.-6691_*32603del Assoc w R - Interim
c.-12945_*26284del Assoc w R - Interim
c.-571_*21383del Assoc w R - Interim
c.-325_*12343del Assoc w R - Interim
c.-13599_*8855del Assoc w R - Interim
c.-37785_*5546del Assoc w R - Interim
para-aminosalicylic_acid thyA c.-6983_*15025del Mutation from literature
c.-44139_*3051del Mutation from literature
delamanid fbiD c.-15370_*12235del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-14370_*29166del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-1360_*17485del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-32699_*15799del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-26753_*4098del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-10121_*34265del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-14552_*17750del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-11839_*28131del Assoc w R - Interim Confers DLM-PMD cross-resistance
bedaquiline pepQ c.-9597_*35883del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-6691_*32603del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-12945_*26284del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-571_*21383del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-325_*12343del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-13599_*8855del Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.-37785_*5546del 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 1880249 c.-37690_*7765del transcript_ablation 0.96 capreomycin Assoc w R
tlyA 1881293 c.-36646_*331del transcript_ablation 0.97 capreomycin Assoc w R
tlyA 1890474 c.-27465_*9198del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1897747 c.-20192_*4058del transcript_ablation 0.9 capreomycin Assoc w R
tlyA 1903309 c.-14630_*27615del transcript_ablation 0.92 capreomycin Assoc w R
tlyA 1904937 c.-13002_*7098del transcript_ablation 0.94 capreomycin Assoc w R
pncA 2261525 c.-13885_*27155del transcript_ablation 0.91 pyrazinamide Assoc w R
pncA 2267586 c.-27535_*21094del transcript_ablation 0.93 pyrazinamide Assoc w R
pncA 2267880 c.-8342_*20800del transcript_ablation 0.91 pyrazinamide Assoc w R
pepQ 2823416 c.-9597_*35883del 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 2826696 c.-6691_*32603del transcript_ablation 0.92 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 2833015 c.-12945_*26284del transcript_ablation 0.95 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 2837916 c.-571_*21383del transcript_ablation 0.92 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 2846956 c.-325_*12343del 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 2850444 c.-13599_*8855del 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 2853753 c.-37785_*5546del transcript_ablation 0.95 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 3058654 c.-6983_*15025del transcript_ablation 0.94 para-aminosalicylic_acid Mutation from literature
thyA 3070628 c.-44139_*3051del transcript_ablation 0.94 para-aminosalicylic_acid Mutation from literature
fbiD 3323747 c.-15370_*12235del transcript_ablation 0.93 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3324747 c.-14370_*29166del transcript_ablation 0.93 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3337757 c.-1360_*17485del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3607843 c.-32699_*15799del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3613789 c.-26753_*4098del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3630421 c.-10121_*34265del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3972291 c.-14552_*17750del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3975004 c.-11839_*28131del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4308945 c.-12201_*17058del transcript_ablation 0.96 ethionamide Assoc w R
ethA 4310329 c.-26066_*15674del transcript_ablation 0.97 ethionamide Assoc w R
ethA 4313472 c.372_*12531del frameshift_variant&stop_lost&splice_region_variant 0.93 ethionamide Assoc w R
ethA 4319577 c.-18092_*6426del transcript_ablation 0.97 ethionamide Assoc w R
ethA 4320024 c.-2103_*5979del transcript_ablation 0.96 ethionamide Assoc w R
gid 4391097 c.-2365_*16430del transcript_ablation 0.95 streptomycin Assoc w R
gid 4401282 c.150_*6245del frameshift_variant&stop_lost&splice_region_variant 0.97 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 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620133 c.244_*1817del stop_lost&conservative_inframe_deletion&splice_region_variant 0.92 capreomycin
amikacin
kanamycin
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
atpE 1458697 c.-2347_*21354del transcript_ablation 0.91 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.99 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1663874 c.-9565_*12077del transcript_ablation 0.93 ethionamide
isoniazid
fabG1 1667008 c.-6431_*29737del transcript_ablation 0.91 ethionamide
isoniazid
rpsA 1823638 c.-9903_*13103del transcript_ablation 0.92 pyrazinamide Uncertain significance
tsnR 1847641 c.-5964_*22228del transcript_ablation 0.98 linezolid Uncertain significance
tsnR 1851751 c.-1854_*29363del transcript_ablation 0.96 linezolid Uncertain significance
tlyA 1911351 c.-6588_630del conservative_inframe_deletion 0.91 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2017864 c.1456_*44944del exon_loss_variant 0.96 streptomycin
kanamycin
capreomycin
amikacin
bacA 2036180 c.-4178_*26628del transcript_ablation 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2038494 c.-12508_*24314del transcript_ablation 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2048414 c.-17500_*14394del transcript_ablation 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2051222 c.-4564_*11586del transcript_ablation 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
ndh 2090703 c.-23068_*10947del transcript_ablation 0.91 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2138773 c.1819_*15115del stop_lost&conservative_inframe_deletion&splice_region_variant 0.95 isoniazid
PPE35 2154932 c.-618_*12716del transcript_ablation 0.92 pyrazinamide Uncertain significance
PPE35 2164971 c.2033_*2677del frameshift_variant&stop_lost&splice_region_variant 0.96 pyrazinamide Uncertain significance
PPE35 2170425 c.-14117_187del frameshift_variant&start_lost 0.92 pyrazinamide Uncertain significance
Rv1979c 2192832 c.-16310_*28886del transcript_ablation 0.93 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2211876 c.-24384_*9842del transcript_ablation 0.91 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222979 c.-19750_185del frameshift_variant 0.93 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
kasA 2499543 c.-18571_*15857del transcript_ablation 0.93 isoniazid
eis 2711516 c.-30676_*2607del transcript_ablation 0.94 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2775305 c.-30171_*7060del transcript_ablation 0.95 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2680 2961700 c.-34404_*14481del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2961890 c.-34214_*7415del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2967513 c.-28591_*9250del transcript_ablation 0.94 capreomycin Uncertain significance
Rv2680 2973543 c.-22561_*4723del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2981310 c.-14794_*30851del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2988110 c.-7994_*16328del transcript_ablation 0.95 capreomycin Uncertain significance
Rv2680 2989345 c.-6759_*6525del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2989694 c.-6410_*24469del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2752c 3048034 c.-2739_*16480del transcript_ablation 0.95 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3078468 c.-8351_*19649del transcript_ablation 0.95 cycloserine
Rv3083 3443758 c.-4745_*15249del transcript_ablation 0.94 ethionamide Uncertain significance
whiB7 3542516 c.-21625_*25884del transcript_ablation 0.95 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3560396 c.-30667_*8004del transcript_ablation 0.95 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3584921 c.676_*27037del stop_lost&conservative_inframe_deletion&splice_region_variant 0.96 pyrazinamide
Rv3236c 3589496 c.-23242_*22462del transcript_ablation 0.95 pyrazinamide Uncertain significance
Rv3236c 3589736 c.-12934_*22222del transcript_ablation 0.98 pyrazinamide Uncertain significance
lpqB 3612539 c.-1381_*10619del transcript_ablation 0.97 bedaquiline
rifampicin Uncertain significance
lpqB 3613024 c.-7541_*10134del transcript_ablation 0.95 bedaquiline
rifampicin Uncertain significance
lpqB 3619038 c.-5572_*4120del transcript_ablation 0.96 bedaquiline
rifampicin Uncertain significance
alr 3813166 c.-7699_*27027del transcript_ablation 0.96 cycloserine
alr 3829362 c.-15467_*10831del transcript_ablation 0.95 cycloserine
alr 3835814 c.-7220_*4379del transcript_ablation 0.94 cycloserine
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
rpoA 3875523 c.-29578_*1940del transcript_ablation 0.94 rifampicin
clpC1 4001723 c.638_*36434del frameshift_variant&stop_lost&splice_region_variant 0.95 pyrazinamide
panD 4015435 c.-4749_*28426del transcript_ablation 0.96 pyrazinamide Uncertain significance
panD 4037039 c.-3179_*6822del transcript_ablation 0.96 pyrazinamide Uncertain significance
glpK 4105655 c.1416_*32546del frameshift_variant&stop_lost&splice_region_variant 0.97 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4130793 c.-34991_*7408del transcript_ablation 0.97 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4137091 c.-43934_*1110del transcript_ablation 0.96 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4137104 c.-4913_*1097del transcript_ablation 0.96 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4265240 c.-34733_*1712del transcript_ablation 0.96 ethambutol Uncertain significance
ethA 4328419 c.-946G>A upstream_gene_variant 1.0 ethionamide
whiB6 4331888 c.-19268_*6282del transcript_ablation 0.96 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