TB-Profiler result

Run: ERR1633838
Summary

Run ID: ERR1633838

Sample name:

Date: 2024-10-04T21:36:33.637476

Number of reads: 2611371

Percentage reads mapped: 99.53

Median coverage: 46.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 0.99
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
ethambutol
pyrazinamide pncA c.-9057_*6193del Assoc w R
streptomycin gid c.-1242_*22145del Assoc w R
c.-348_*13987del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-41473_*1914del Assoc w R
c.-38509_*8538del Assoc w R
c.-35245_*3163del Assoc w R
c.-33000_*566del Assoc w R
c.-27971_*5003del Assoc w R
c.-27611_*8695del Assoc w R
c.-13290_*9172del Assoc w R
c.-2687_*8678del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-25940_*5953del Assoc w R
ethR p.Phe110Leu Uncertain significance Mutation from literature
clofazimine
para-aminosalicylic_acid thyA c.-2901_*15708del Mutation from literature
delamanid fbiD c.-14258_*750del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-11355_*10186del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-153_*2815del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-23521_*21105del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-23429_*14686del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-18072_*11663del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-2862_*1994del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-23128_*6932del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-3207_*45902del 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
tlyA 1876466 c.-41473_*1914del transcript_ablation 0.97 capreomycin Assoc w R
tlyA 1879430 c.-38509_*8538del transcript_ablation 0.98 capreomycin Assoc w R
tlyA 1882694 c.-35245_*3163del transcript_ablation 0.96 capreomycin Assoc w R
tlyA 1884939 c.-33000_*566del transcript_ablation 0.96 capreomycin Assoc w R
tlyA 1889968 c.-27971_*5003del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1890328 c.-27611_*8695del transcript_ablation 0.96 capreomycin Assoc w R
tlyA 1904649 c.-13290_*9172del transcript_ablation 0.93 capreomycin Assoc w R
tlyA 1915252 c.-2687_*8678del transcript_ablation 0.97 capreomycin Assoc w R
pncA 2282487 c.-9057_*6193del transcript_ablation 0.91 pyrazinamide Assoc w R
thyA 3057971 c.-2901_*15708del transcript_ablation 0.93 para-aminosalicylic_acid Mutation from literature
fbiD 3324859 c.-14258_*750del transcript_ablation 0.96 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3327762 c.-11355_*10186del 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 3338964 c.-153_*2815del 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 3617021 c.-23521_*21105del 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 3617113 c.-23429_*14686del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3622470 c.-18072_*11663del 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 3637680 c.-2862_*1994del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3963715 c.-23128_*6932del 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 3983636 c.-3207_*45902del transcript_ablation 0.96 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4320050 c.-25940_*5953del transcript_ablation 0.98 ethionamide Assoc w R
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide Uncertain significance Mutation from literature
gid 4385382 c.-1242_*22145del transcript_ablation 0.95 streptomycin Assoc w R
gid 4393540 c.-348_*13987del transcript_ablation 0.94 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8512 p.Val404Gly missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_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
rplC 800200 c.-609C>G upstream_gene_variant 1.0 linezolid
rplC 800889 c.81C>A synonymous_variant 1.0 linezolid Not assoc w R - Interim
sigE 1360207 c.-4205_*5412del transcript_ablation 0.9 pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1667068 c.-7133_*12032del transcript_ablation 0.91 isoniazid
ethionamide
rpsA 1813527 c.-20014_*26437del transcript_ablation 0.94 pyrazinamide Uncertain significance
tsnR 1837498 c.-16107_*26087del transcript_ablation 0.94 linezolid Uncertain significance
tsnR 1845051 c.-8554_*28966del transcript_ablation 0.96 linezolid Uncertain significance
tsnR 1848681 c.-4924_*23846del transcript_ablation 0.98 linezolid Uncertain significance
tsnR 1848768 c.-4837_*35443del transcript_ablation 0.94 linezolid Uncertain significance
tsnR 1849203 c.-4402_*41476del transcript_ablation 0.92 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.96 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2046191 c.-24161_*16617del transcript_ablation 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
bacA 2061329 c.-23933_*1479del transcript_ablation 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
ndh 2072336 c.-4968_*29314del transcript_ablation 0.92 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2168303 c.2310G>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1979c 2217808 c.-38545_*3910del 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 2501885 c.-16229_*16096del transcript_ablation 0.92 isoniazid
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
eis 2688827 c.-6542_*25296del transcript_ablation 0.94 kanamycin Uncertain significance
amikacin Uncertain significance
folC 2737346 c.-8350_*8788del transcript_ablation 0.92 para-aminosalicylic_acid
Rv2477c 2754188 c.-11755_*28177del 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 2766719 c.-31381_*15646del transcript_ablation 0.94 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2775417 c.-8423_*6948del transcript_ablation 0.94 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2776799 c.-20042_*5566del 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
Rv2680 2959071 c.-37033_*1642del transcript_ablation 0.94 capreomycin Uncertain significance
ribD 2967153 c.-19685_*2018del transcript_ablation 0.96 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.34 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3600296 c.200_*11662del frameshift_variant&stop_lost&splice_region_variant 0.95 pyrazinamide Uncertain significance
lpqB 3616812 c.-990_*6346del transcript_ablation 0.93 rifampicin Uncertain significance
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3813148 c.-14926_*27045del transcript_ablation 0.96 cycloserine
alr 3840263 c.1158C>T synonymous_variant 1.0 cycloserine
rpoA 3871415 c.-39459_*6048del transcript_ablation 0.96 rifampicin
rpoA 3878379 c.-23760_128del frameshift_variant&start_lost 0.93 rifampicin
panD 4018481 c.-6627_*25380del transcript_ablation 0.93 pyrazinamide Uncertain significance
panD 4023218 c.-22950_*20643del transcript_ablation 0.98 pyrazinamide Uncertain significance
panD 4026107 c.-10948_*17754del transcript_ablation 0.94 pyrazinamide Uncertain significance
panD 4037569 c.-10358_*6292del transcript_ablation 0.93 pyrazinamide Uncertain significance
glpK 4137954 c.-27809_*247del transcript_ablation 0.95 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embA 4222212 c.-21020_*3856del transcript_ablation 0.97 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
aftB 4259276 c.-38870_*7676del transcript_ablation 0.95 ethambutol Uncertain significance
aftB 4261047 c.-7708_*5905del transcript_ablation 0.94 ethambutol Uncertain significance
aftB 4267091 c.1746C>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4268151 c.-19877_685del frameshift_variant&start_lost 0.95 ethambutol Uncertain significance
ubiA 4269136 c.-15210_697del frameshift_variant&start_lost 0.92 ethambutol
whiB6 4330096 c.-13555_*8074del transcript_ablation 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin