TB-Profiler result

Run: ERR3273190
Summary

Run ID: ERR3273190

Sample name:

Date: 2024-04-16T02:17:08.964077

Number of reads: 2507510

Percentage reads mapped: 99.51

Median coverage: 75.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala 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.Asp94Ala missense_variant 0.98 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761101 p.Gln432Pro missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.98 ethionamide Uncertain significance
Rv0565c 657110 p.Trp121Gly missense_variant 1.0 ethionamide
nusG 734658 c.405A>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.99 rifampicin Uncertain significance
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.99 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 0.98 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289595 c.-354A>G upstream_gene_variant 0.99 pyrazinamide
eis 2714693 p.Ser214Pro missense_variant 0.98 amikacin
kanamycin
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.98 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 1.0 pyrazinamide Not assoc w R
glpK 4138372 c.1382_1383dupCC frameshift_variant 0.17 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.16 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 1.0 ethambutol Not assoc w R
ubiA 4269865 c.-32G>C upstream_gene_variant 1.0 ethambutol
ethR 4327300 c.-249G>A upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R