TB-Profiler result

Run: SRR998709
Summary

Run ID: SRR998709

Sample name:

Date: 2024-10-05T03:53:42.422773

Number of reads: 3245025

Percentage reads mapped: 99.47

Median coverage: 72.0

Strain: lineage4.1.2.1;lineage6.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.9
lineage6.3 West-Africa 2 RD702 0.07
lineage4.1.2 Euro-American None 0.94
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.93
lineage4 Euro-American None 0.94
lineage6 West-Africa 2 RD702 0.07
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 0.9 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
dnaA 1302 c.1302C>T synonymous_variant 0.95 isoniazid Not assoc w R - Interim
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.92 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.96 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.95 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.88 rifampicin Not assoc w R
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
fbiC 1302899 c.-32A>G upstream_gene_variant 0.12 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.13 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.13 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
bacA 2062922 p.Ile603Val missense_variant 0.12 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.13 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.14 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.94 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.25 capreomycin Uncertain significance
ald 3086728 c.-92C>T upstream_gene_variant 0.16 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
mtrA 3627756 c.-407A>T upstream_gene_variant 0.95 rifampicin
bedaquiline
clpC1 4038408 p.Pro766Leu missense_variant 0.94 pyrazinamide Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.87 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.13 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.88 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.14 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.15 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