TB-Profiler result

Run: ERR2228813
Summary

Run ID: ERR2228813

Sample name:

Date: 2024-03-26T18:02:35.572035

Number of reads: 1355835

Percentage reads mapped: 81.1

Median coverage: 28.0

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 0.99
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
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
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 0.19 amikacin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
capreomycin 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
rpoB 762920 c.3114C>T synonymous_variant 0.16 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 0.96 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.53 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 0.52 capreomycin
linezolid
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.62 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 3448497 c.-6_*1408del transcript_ablation 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