TB-Profiler result

Run: ERR4812453
Summary

Run ID: ERR4812453

Sample name:

Date: 2024-10-04T03:40:16.592315

Number of reads: 4955266

Percentage reads mapped: 99.71

Median coverage: 162.0

Strain: lineage4.1.2.1;lineage4.4.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.24
lineage4.1.2 Euro-American None 0.25
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.21
lineage4.4.1 Euro-American (S-type) None 0.76
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.79
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin gid p.Gln125* 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
pncA 2289252 c.-11A>G upstream_gene_variant 0.11 pyrazinamide Assoc w R
gid 4407830 p.Gln125* stop_gained 0.22 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
dnaA 309 c.309G>C synonymous_variant 0.82 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
Rv0010c 13502 c.57G>T synonymous_variant 0.75 isoniazid Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.26 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.29 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.18 ethionamide Uncertain significance
hadA 731980 c.51C>T synonymous_variant 0.79 isoniazid Not assoc w R - Interim
rpoB 760115 c.309C>T synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.33 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475227 n.1572dupA non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
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
ndh 2102990 p.Val18Ala missense_variant 0.76 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.78 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 0.22 isoniazid
pepQ 2860286 p.Val45Leu missense_variant 0.79 bedaquiline Uncertain significance
clofazimine Uncertain significance
ribD 2986827 c.-12G>A upstream_gene_variant 0.2 para-aminosalicylic_acid
Rv2752c 3066389 c.-198C>T upstream_gene_variant 0.76 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
glpK 4140002 c.-247C>A upstream_gene_variant 0.25 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4238963 c.-900C>T upstream_gene_variant 0.81 ethambutol Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.18 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 0.22 ethambutol Not assoc w R
whiB6 4338460 p.Met21Thr missense_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338520 p.Met1? start_lost 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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