TB-Profiler result

Run: SRR6785497
Summary

Run ID: SRR6785497

Sample name:

Date: 2024-10-05T06:31:50.473213

Number of reads: 3727843

Percentage reads mapped: 97.84

Median coverage: 49.0

Strain: lineage4.3.3

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 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 1.0
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8527 p.Arg409Gln missense_variant 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765967 c.2598C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.14 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
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
rpsL 781736 c.177T>C synonymous_variant 0.12 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.13 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.12 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.12 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.12 streptomycin
rpsL 781772 c.213C>A synonymous_variant 0.16 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.17 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.17 streptomycin
fbiC 1303095 c.165G>A synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673380 c.-822C>G upstream_gene_variant 0.27 isoniazid
ethionamide
rpsA 1834836 p.Met432Thr missense_variant 1.0 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 1.0 isoniazid Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.4 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.41 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.98 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.89 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.98 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625705 c.909C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625714 c.-804C>T upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3625720 c.894G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625729 c.885A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625735 c.-825C>T upstream_gene_variant 0.16 rifampicin
bedaquiline
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.36 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.44 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.44 ethambutol Uncertain significance
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 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.98 streptomycin Not assoc w R
gid 4408174 p.Ala10Gly missense_variant 0.97 streptomycin Uncertain significance