TB-Profiler result

Run: SRR14807564
Summary

Run ID: SRR14807564

Sample name:

Date: 2024-04-16T10:53:14.541794

Number of reads: 2638021

Percentage reads mapped: 99.73

Median coverage: 85.0

Strain: lineage4.3.3;lineage4.8

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 0.38
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.6
lineage4.3.3 Euro-American (LAM) RD115 0.41
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.68 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.61 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.33 rifampicin Not assoc w R
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
Rv1129c 1253304 p.Asn411Tyr missense_variant 0.39 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834836 p.Met432Thr missense_variant 0.51 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.39 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.63 pyrazinamide Not assoc w R
PPE35 2168247 p.Leu789Arg missense_variant 0.54 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289952 c.-711C>G upstream_gene_variant 0.55 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.41 isoniazid
ribD 2986701 c.-138G>A upstream_gene_variant 0.44 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.51 capreomycin
Rv2752c 3067135 c.-944C>T upstream_gene_variant 0.37 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.45 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.38 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.6 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.43 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877546 p.Ala321Gly missense_variant 0.16 rifampicin
rpoA 3878783 c.-276C>T upstream_gene_variant 0.55 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.41 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.54 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248090 p.Tyr526Ser missense_variant 0.39 ethambutol
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 4338732 c.-211C>T upstream_gene_variant 0.44 capreomycin
amikacin
kanamycin
gid 4407720 c.483C>G synonymous_variant 0.43 streptomycin Not assoc w R - Interim
gid 4408156 p.Leu16Arg missense_variant 0.54 streptomycin Not assoc w R