TB-Profiler result

Run: ERR216971
Summary

Run ID: ERR216971

Sample name:

Date: 2024-10-05T03:02:46.819413

Number of reads: 1354236

Percentage reads mapped: 98.74

Median coverage: 23.0

Strain: lineage4.1.2;lineage4.2.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.26
lineage4.1 Euro-American None 0.66
lineage4.1.2 Euro-American None 0.67
lineage4.2 Euro-American None 0.23
lineage4 Euro-American None 1.0
lineage4.2.2.2 Euro-American (Ural) None 0.2
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
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
katG 2155168 p.Ser315Thr missense_variant 0.57 isoniazid Assoc w R High-level resistance
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 7323 p.Pro8Ala missense_variant 0.67 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 8688 p.Ala463Ser missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.72 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.33 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
ccsA 619877 c.-14G>A upstream_gene_variant 0.43 kanamycin
capreomycin
amikacin
Rv0565c 656832 c.639G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.75 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.5 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.77 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.93 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776659 p.Asp608Asn missense_variant 0.58 bedaquiline Uncertain significance
clofazimine Uncertain significance
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 1853569 c.-37C>T upstream_gene_variant 0.83 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.38 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2064130 p.Gly200Ala missense_variant 0.71 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2168501 p.Phe704Leu missense_variant 0.72 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.68 isoniazid
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.37 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.26 cycloserine
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 3625581 c.1033C>A synonymous_variant 0.81 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.71 ethambutol Not assoc w R
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