TB-Profiler result

Run: ERR137199
Summary

Run ID: ERR137199

Sample name:

Date: 2024-10-04T06:48:38.570259

Number of reads: 10124326

Percentage reads mapped: 99.59

Median coverage: 219.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.2
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.79
lineage4.2.1 Euro-American (TUR) None 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin gid c.52delC Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.23 ethambutol Assoc w R
gid 4408150 c.52delC frameshift_variant 0.19 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 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.21 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13624 c.-66C>T upstream_gene_variant 0.73 isoniazid 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
rplC 800204 c.-605T>C upstream_gene_variant 0.18 linezolid
embR 1417985 c.-638C>A upstream_gene_variant 0.8 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1833461 c.-81T>C upstream_gene_variant 0.23 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.19 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.23 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.79 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.24 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.72 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.23 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.23 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249007 p.Pro832Ser missense_variant 0.19 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 0.21 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.23 ethionamide
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 0.21 kanamycin
capreomycin
amikacin