TB-Profiler result

Run: ERR2228965
Summary

Run ID: ERR2228965

Sample name:

Date: 2024-04-15T06:29:06.153289

Number of reads: 299839

Percentage reads mapped: 60.78

Median coverage: 7.0

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 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 rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.92 kanamycin Assoc w R
capreomycin Assoc w R
amikacin 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
rpoC 763570 c.201G>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.86 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.86 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.91 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73 capreomycin Not assoc w R
linezolid Uncertain significance
PPE35 2168728 p.Gly629Arg missense_variant 1.0 pyrazinamide Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
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