TB-Profiler result

Run: SRR998711
Summary

Run ID: SRR998711

Sample name:

Date: 2024-03-25T22:20:31.164603

Number of reads: 3251416

Percentage reads mapped: 99.48

Median coverage: 72.0

Strain: lineage4.1.2.1

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 0.92
lineage4.1.2 Euro-American None 0.93
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.9
lineage4 Euro-American None 0.95
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 0.87 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 0.9 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.85 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619628 c.-263G>A upstream_gene_variant 0.12 capreomycin
amikacin
kanamycin
Rv0565c 657269 p.Ser68Pro missense_variant 0.91 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.14 ethionamide
rpoB 760115 c.309C>T synonymous_variant 0.87 rifampicin Not assoc w R
rpoB 760969 p.Ser388Leu missense_variant 0.11 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.87 rifampicin Not assoc w R
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
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 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.14 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.11 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.86 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.12 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.34 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.14 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.91 bedaquiline
rifampicin
clpC1 4038408 p.Pro766Leu missense_variant 0.95 pyrazinamide Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.96 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 0.94 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin