TB-Profiler result

Run: ERR036211

Summary

Run ID: ERR036211

Sample name:

Date: 2024-04-15T15:49:40.729765

Number of reads: 1168771

Percentage reads mapped: 93.55

Median coverage: 20.0

Strain: lineage1.1.3.2;lineage4.3.4.2.1;lineage4.9

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 0.4
lineage1.1.3 Indo-Oceanic RD239 0.14
lineage1.1.3.2 Indo-Oceanic RD239 0.07
lineage1.1 Indo-Oceanic RD239 0.06
lineage4 Euro-American None 0.69
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.51
lineage1 Indo-Oceanic RD239 0.19
lineage4.9 Euro-American (H37Rv-like) None 0.09
lineage4.3.4 Euro-American (LAM) RD174 0.56
lineage4.3.4.2 Euro-American (LAM) RD174 0.42
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 0.3 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 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.41 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.35 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.59 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.32 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.29 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854045 p.Tyr147Cys missense_variant 0.39 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.87 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.32 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.42 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.38 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3064632 c.1560C>T synonymous_variant 0.32 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.47 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.88 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.5 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.9 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
whiB6 4338603 c.-82C>T upstream_gene_variant 0.35 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.84 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.55 streptomycin Not assoc w R