TB-Profiler result

Run: ERR4829865
Summary

Run ID: ERR4829865

Sample name:

Date: 2024-10-05T04:39:33.707053

Number of reads: 1949738

Percentage reads mapped: 98.17

Median coverage: 54.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
isoniazid
ethambutol embA c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asn499Lys Uncertain significance Mutation from literature
gyrA p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Asn499Lys Uncertain significance Mutation from literature
gyrA p.Asp94Tyr Assoc w R
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
gyrB 6736 p.Asn499Lys missense_variant 0.83 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7581 p.Asp94Tyr missense_variant 0.36 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.47 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.5 streptomycin Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 0.45 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.58 ethambutol 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490661 c.-121_-116delGCGAGC upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
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
Rv1258c 1406556 p.Trp262* stop_gained 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473012 n.1167G>A non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102290 p.Asp251Glu missense_variant 1.0 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
fbiA 3640901 p.Gln120Arg missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 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