TB-Profiler result

Run: SRR9738493
Summary

Run ID: SRR9738493

Sample name:

Date: 2024-04-14T22:53:15.510515

Number of reads: 2568851

Percentage reads mapped: 99.51

Median coverage: 79.0

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.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Ala146Val Assoc w R
streptomycin rpsL p.Lys88Gln Assoc w R - Interim
gid p.Gln125* Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ser447Phe Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Ser447Phe Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.752dupG Assoc w R
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 6579 p.Ser447Phe missense_variant 1.0 moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R - Interim
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781821 p.Lys88Gln missense_variant 1.0 streptomycin Assoc w R - Interim
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide Assoc w R
gid 4407830 p.Gln125* stop_gained 1.0 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 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13543 p.Trp6Arg missense_variant 1.0 isoniazid Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 765008 p.Leu547Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 766085 p.Pro906Ala missense_variant 1.0 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
atpE 1460992 c.-53A>C upstream_gene_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475953 n.2296A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
ald 3087065 c.247_248dupGG frameshift_variant 1.0 cycloserine
Rv3083 3448508 c.6_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
whiB7 3568547 p.Ser45Arg missense_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
alr 3840952 p.Lys157Glu missense_variant 1.0 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 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