TB-Profiler result

Run: SRR10305972
Summary

Run ID: SRR10305972

Sample name:

Date: 2024-10-04T02:13:49.387963

Number of reads: 2376160

Percentage reads mapped: 99.56

Median coverage: 124.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.99
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.His57Gln Assoc w R - Interim
streptomycin gid c.517delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
pncA 2289071 p.His57Gln missense_variant 0.99 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol Assoc w R
gid 4407685 c.517delG frameshift_variant 0.99 streptomycin Assoc w R
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 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8379 p.Gln360Lys missense_variant 0.99 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576242 p.Gly299Arg missense_variant 0.99 isoniazid
ethionamide
ccsA 620029 c.139C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
rpoC 764840 p.Ile491Val missense_variant 0.99 rifampicin Uncertain significance
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 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854030 p.Arg142Leu missense_variant 1.0 linezolid Uncertain significance
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 2155556 p.Gly186Ser missense_variant 1.0 isoniazid
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726142 c.-51G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
clpC1 4040498 c.207G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138387 p.Ala457Pro missense_variant 0.97 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4241860 c.1998C>T synonymous_variant 0.99 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243760 p.Asp176Glu missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338593 c.-72C>G upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
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 4408356 c.-154G>A upstream_gene_variant 1.0 streptomycin