TB-Profiler result

Run: SRR20958128
Summary

Run ID: SRR20958128

Sample name:

Date: 2024-04-16T01:44:32.108873

Number of reads: 13358523

Percentage reads mapped: 99.88

Median coverage: 371.0

Strain: lineage4.3.3;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 0.47
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.56
lineage4.3.3 Euro-American (LAM) RD115 0.45
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 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.48 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 0.46 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761880 p.Ala692Thr missense_variant 0.47 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.42 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.5 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.44 streptomycin Not assoc w R
sigE 1364427 c.15C>T synonymous_variant 0.45 pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.42 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.47 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.44 capreomycin Not assoc w R
katG 2154459 c.1653C>T synonymous_variant 0.54 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.48 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.53 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.52 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.47 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.45 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878614 c.-107A>C upstream_gene_variant 0.14 rifampicin
rpoA 3878619 c.-112A>C upstream_gene_variant 0.13 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
panD 4044824 c.-543C>G upstream_gene_variant 0.47 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.24 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.41 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.21 ethambutol
whiB6 4338593 c.-73delT upstream_gene_variant 0.47 capreomycin
amikacin
kanamycin
whiB6 4338596 c.-75G>C upstream_gene_variant 0.47 capreomycin
amikacin
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 0.48 capreomycin
amikacin
kanamycin
gid 4407720 c.483C>G synonymous_variant 0.51 streptomycin Not assoc w R - Interim
gid 4408156 p.Leu16Arg missense_variant 0.42 streptomycin Not assoc w R