TB-Profiler result

Run: ERR4817847
Summary

Run ID: ERR4817847

Sample name:

Date: 2024-10-05T08:38:30.466757

Number of reads: 2502312

Percentage reads mapped: 93.18

Median coverage: 74.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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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 0.97
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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
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 412 p.Ala138Thr missense_variant 0.99 isoniazid Uncertain significance
gyrB 5524 c.285C>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13442 p.Leu39Phe missense_variant 1.0 isoniazid Uncertain significance
rpoB 760101 c.295T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760112 c.306T>C synonymous_variant 0.13 rifampicin
rpoB 760121 c.315T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760181 c.375T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.13 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.13 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.13 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766312 c.2943T>G synonymous_variant 0.12 rifampicin
rpoC 766345 c.2976T>C synonymous_variant 0.17 rifampicin
rpoC 766348 c.2979A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766363 c.2994G>C synonymous_variant 0.16 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.19 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.18 rifampicin
rpoC 766390 c.3021C>T synonymous_variant 0.12 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.15 rifampicin
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
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.96 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.93 ethionamide Uncertain significance
clpC1 4038878 c.1827A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.13 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247470 c.957T>C synonymous_variant 0.16 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.13 ethambutol
embB 4249354 c.2841G>C synonymous_variant 0.98 ethambutol Not assoc w R - Interim
whiB6 4338590 c.-69A>T upstream_gene_variant 0.97 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