TB-Profiler result

Run: SRR1162720
Summary

Run ID: SRR1162720

Sample name:

Date: 2024-10-04T16:45:35.925147

Number of reads: 2019161

Percentage reads mapped: 98.98

Median coverage: 44.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-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 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Val170Phe Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide pncA p.Thr142Lys Assoc w R - Interim
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
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288817 p.Thr142Lys missense_variant 0.45 pyrazinamide Assoc w R - Interim
embB 4247574 p.Asp354Ala missense_variant 1.0 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
rpoC 765950 p.Ala861Thr missense_variant 1.0 rifampicin Uncertain significance
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
rpsL 781676 c.117C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
PPE35 2168149 p.Pro822Ser missense_variant 1.0 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243700 c.468C>T synonymous_variant 1.0 ethambutol
embB 4248222 p.Pro570Leu missense_variant 1.0 ethambutol
embB 4249354 c.2841G>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ubiA 4269713 p.Gly41Arg missense_variant 1.0 ethambutol 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
gid 4407911 p.Thr98Ala missense_variant 1.0 streptomycin
gid 4407913 p.Arg97His missense_variant 1.0 streptomycin Uncertain significance