TB-Profiler result

Run: SRR7645855
Summary

Run ID: SRR7645855

Sample name:

Date: 2024-10-04T10:02:40.943348

Number of reads: 4947572

Percentage reads mapped: 99.62

Median coverage: 98.0

Strain: lineage2.2;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
lineage2.2 East-Asian (Beijing) RD105;RD207 0.05
lineage4 Euro-American None 0.95
lineage4.8 Euro-American (mainly T) RD219 0.94
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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.93 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.97 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.13 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
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.95 capreomycin Not assoc w R
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 0.93 pyrazinamide Not assoc w R
PPE35 2168247 p.Leu789Arg missense_variant 0.91 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289952 c.-711C>G upstream_gene_variant 0.93 pyrazinamide
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.94 capreomycin
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.95 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878783 c.-276C>T upstream_gene_variant 0.9 rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.92 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol 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 0.11 kanamycin
capreomycin
amikacin