TB-Profiler result

Run: ERR2600526
Summary

Run ID: ERR2600526

Sample name:

Date: 2024-10-05T13:52:45.938416

Number of reads: 5867109

Percentage reads mapped: 99.38

Median coverage: 182.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.14
lineage4.1.2 Euro-American None 0.16
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.15
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.85
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 0.13 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
gyrB 6000 p.Pro254Leu missense_variant 0.12 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 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13680 c.-122G>A upstream_gene_variant 0.88 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.19 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.14 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.23 isoniazid
ethionamide
rpoB 760106 c.300G>A synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764175 p.Asp269Gly missense_variant 0.86 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.14 rifampicin Not assoc w R
rpoC 765691 c.2322G>T synonymous_variant 0.33 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 0.19 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.14 linezolid Not assoc w R
tsnR 1854329 p.Val242Phe missense_variant 0.89 linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.86 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 0.17 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.84 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.14 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
ddn 3986815 c.-29G>C upstream_gene_variant 0.86 pretomanid
delamanid
panD 4044824 c.-543C>T upstream_gene_variant 0.2 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 0.14 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 0.2 ethambutol Not assoc w R
whiB6 4338513 c.9C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
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 0.42 kanamycin
capreomycin
amikacin