TB-Profiler result

Run: ERR11465291
Summary

Run ID: ERR11465291

Sample name:

Date: 2024-10-04T06:19:10.875648

Number of reads: 1562517

Percentage reads mapped: 99.6

Median coverage: 28.0

Strain:

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.8
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.81
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 1163 p.Thr388Ile missense_variant 0.27 isoniazid Uncertain significance
dnaA 1285 p.Glu429Lys missense_variant 0.66 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.55 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.58 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.8 streptomycin Not assoc w R
Rv1129c 1253574 p.Leu321Phe missense_variant 0.32 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475552 n.1895G>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
tlyA 1917972 c.33A>G synonymous_variant 0.5 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.96 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783425 c.618C>T synonymous_variant 0.51 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
thyX 3067248 p.Thr233Ile missense_variant 0.79 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.82 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.75 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.83 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.65 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.8 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.62 pyrazinamide Not assoc w R
embA 4245113 c.1881C>T synonymous_variant 0.44 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.8 ethambutol Uncertain significance
ethA 4328245 c.-772C>T upstream_gene_variant 0.5 ethionamide
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 0.92 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R