TB-Profiler result

Run: ERR2229234
Summary

Run ID: ERR2229234

Sample name:

Date: 2024-04-15T01:37:24.816040

Number of reads: 1379208

Percentage reads mapped: 89.04

Median coverage: 27.0

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 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 762080 c.2274G>C synonymous_variant 0.25 rifampicin
rpoB 762086 c.2280G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763504 c.135C>A synonymous_variant 0.24 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.28 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.31 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.29 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.29 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 763578 p.Phe70Tyr missense_variant 0.35 rifampicin
rpoC 763589 p.Ile74Val missense_variant 0.41 rifampicin
rpoC 763622 p.Ala85Ser missense_variant 0.36 rifampicin Uncertain significance
rpoC 763630 c.261G>C synonymous_variant 0.37 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.38 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763647 p.Gly93Ala missense_variant 0.34 rifampicin
rpoC 763655 p.Glu96Lys missense_variant 0.29 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
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
fbiC 1303747 p.Thr273Ala missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.46 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.47 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.71 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.65 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
clpC1 4040057 c.648C>T synonymous_variant 0.23 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R