TB-Profiler result

Run: ERR279534
Summary

Run ID: ERR279534

Sample name:

Date: 2024-10-05T05:50:10.611902

Number of reads: 3132743

Percentage reads mapped: 99.51

Median coverage: 56.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: Other

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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 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
isoniazid
ethambutol
pyrazinamide pncA c.-2771_*36583del Assoc w R
c.-7933_*27111del Assoc w R
c.-38247_*396del Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-38293_*524del Assoc w R
c.-37698_*9573del Assoc w R
c.-34232_*4752del Assoc w R
c.-33288_*516del Assoc w R
c.-31905_*9188del Assoc w R
c.-28388_*9028del Assoc w R
c.-27851_*16207del Assoc w R
c.-15860_*8781del Assoc w R
c.-9223_*8279del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-25909_*22606del Assoc w R
ethR p.Phe110Leu Uncertain significance Mutation from literature
clofazimine
para-aminosalicylic_acid
delamanid
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 1879646 c.-38293_*524del transcript_ablation 0.95 capreomycin Assoc w R
tlyA 1880241 c.-37698_*9573del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1883707 c.-34232_*4752del transcript_ablation 0.93 capreomycin Assoc w R
tlyA 1884651 c.-33288_*516del transcript_ablation 0.95 capreomycin Assoc w R
tlyA 1886034 c.-31905_*9188del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1889551 c.-28388_*9028del transcript_ablation 0.97 capreomycin Assoc w R
tlyA 1890088 c.-27851_*16207del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1902079 c.-15860_*8781del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1908716 c.-9223_*8279del transcript_ablation 0.95 capreomycin Assoc w R
pncA 2252097 c.-2771_*36583del transcript_ablation 0.91 pyrazinamide Assoc w R
pncA 2261569 c.-7933_*27111del transcript_ablation 0.94 pyrazinamide Assoc w R
pncA 2288284 c.-38247_*396del transcript_ablation 0.92 pyrazinamide Assoc w R
ethA 4303397 c.-25909_*22606del transcript_ablation 0.98 ethionamide Assoc w R
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide 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 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
Rv1129c 1239411 c.-8055_*13662del transcript_ablation 0.96 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1258c 1376901 c.-7632_*29179del transcript_ablation 0.9 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1844419 c.-9186_*28775del transcript_ablation 0.95 linezolid Uncertain significance
tsnR 1846941 c.-6664_*34475del transcript_ablation 0.97 linezolid Uncertain significance
tsnR 1848428 c.-5177_*22231del transcript_ablation 0.94 linezolid Uncertain significance
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
ndh 2101036 c.-3268_*614del transcript_ablation 0.91 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2164481 c.1221_*3167del frameshift_variant&stop_lost&splice_region_variant 0.93 pyrazinamide Uncertain significance
PPE35 2167022 c.1244_*626del frameshift_variant&stop_lost&splice_region_variant 0.93 pyrazinamide Uncertain significance
PPE35 2168303 c.2310G>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
folC 2731607 c.1418_*14527del frameshift_variant&stop_lost&splice_region_variant 0.91 para-aminosalicylic_acid
Rv2477c 2781477 c.-18885_*888del transcript_ablation 0.93 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2680 2952008 c.-44096_*1375del transcript_ablation 0.91 capreomycin Uncertain significance
Rv2680 2955145 c.-40959_*3892del transcript_ablation 0.91 capreomycin Uncertain significance
Rv2680 2961559 c.-34545_*1493del transcript_ablation 0.96 capreomycin Uncertain significance
Rv2680 2969403 c.-26701_*4660del transcript_ablation 0.91 capreomycin Uncertain significance
Rv2680 2989622 c.-6482_*15046del transcript_ablation 0.91 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.37 capreomycin Uncertain significance
ald 3083794 c.-3025_*30633del transcript_ablation 0.92 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3431778 c.-16725_*26704del transcript_ablation 0.9 ethionamide Uncertain significance
Rv3236c 3582329 c.-17609_*29629del transcript_ablation 0.95 pyrazinamide Uncertain significance
Rv3236c 3585137 c.624_*26821del frameshift_variant&stop_lost&splice_region_variant 0.95 pyrazinamide Uncertain significance
Rv3236c 3595542 c.559_*16416del stop_lost&conservative_inframe_deletion&splice_region_variant 0.95 pyrazinamide
Rv3236c 3597749 c.-13621_*14209del transcript_ablation 0.94 pyrazinamide Uncertain significance
Rv3236c 3611871 c.-19849_*87del transcript_ablation 0.96 pyrazinamide Uncertain significance
lpqB 3613329 c.-11935_*9829del transcript_ablation 0.94 rifampicin Uncertain significance
bedaquiline
lpqB 3621560 c.-6448_*1598del transcript_ablation 0.9 rifampicin Uncertain significance
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3832830 c.-38303_*7363del transcript_ablation 0.94 cycloserine
alr 3838384 c.-2819_*1809del transcript_ablation 0.96 cycloserine
alr 3840263 c.1158C>T synonymous_variant 1.0 cycloserine
panD 4024238 c.-18799_*19623del transcript_ablation 0.91 pyrazinamide Uncertain significance
panD 4031967 c.-29408_*11894del transcript_ablation 0.95 pyrazinamide Uncertain significance
panD 4037102 c.-3812_*6759del transcript_ablation 0.96 pyrazinamide Uncertain significance
embA 4237081 c.-6151_*12509del transcript_ablation 0.94 ethambutol Uncertain significance
embA 4237907 c.-5325_*40536del transcript_ablation 0.94 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 4251059 c.-19766_*15893del transcript_ablation 0.93 ethambutol Uncertain significance
aftB 4267091 c.1746C>A synonymous_variant 0.98 ethambutol Not assoc w R - Interim
aftB 4268711 c.-47374_125del frameshift_variant&start_lost 0.93 ethambutol 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