TB-Profiler result

Run: ERR036224
Summary

Run ID: ERR036224

Sample name:

Date: 2024-10-03T21:44:11.238140

Number of reads: 1096221

Percentage reads mapped: 95.69

Median coverage: 18.0

Strain: lineage1.1.3;lineage4.3.4.2.1

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 0.64
lineage1.1.3 Indo-Oceanic RD239 0.08
lineage1.1 Indo-Oceanic RD239 0.23
lineage4 Euro-American None 0.72
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.39
lineage1 Indo-Oceanic RD239 0.16
lineage4.3.4 Euro-American (LAM) RD174 0.38
lineage4.3.4.2 Euro-American (LAM) RD174 0.4
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
gyrB 6140 p.Val301Leu missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.45 ethionamide
rpoC 764995 c.1626C>G synonymous_variant 0.42 rifampicin Not assoc w R
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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.21 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.36 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.36 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.33 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.3 bedaquiline Not assoc w R - Interim
clofazimine 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
ald 3086788 c.-32T>C upstream_gene_variant 0.86 cycloserine
alr 3840719 c.702A>G synonymous_variant 0.52 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.63 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.29 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.38 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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 0.88 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.36 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.64 streptomycin Not assoc w R