TB-Profiler result

Run: SRR21798486
Summary

Run ID: SRR21798486

Sample name:

Date: 2024-04-16T01:46:03.522764

Number of reads: 1458479

Percentage reads mapped: 99.71

Median coverage: 44.0

Strain: 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 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
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 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.94 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 2167965 p.Ala883Gly missense_variant 0.2 pyrazinamide
PPE35 2167967 c.2646A>C synonymous_variant 0.19 pyrazinamide
PPE35 2168149 p.Pro822Ser missense_variant 0.98 pyrazinamide Not assoc w R
PPE35 2169902 c.709_711delCTGinsTC frameshift_variant&synonymous_variant 0.21 pyrazinamide Uncertain significance
PPE35 2170147 p.Ser156Ala missense_variant 0.18 pyrazinamide
PPE35 2170157 c.454_456delGCGinsTT frameshift_variant&missense_variant 0.19 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ribD 2986912 p.Asp25Ala missense_variant 1.0 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448322 c.-182G>A upstream_gene_variant 1.0 ethionamide
alr 3841546 c.-126C>A upstream_gene_variant 0.13 cycloserine
rpoA 3878707 c.-200C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
embC 4240801 c.939C>T synonymous_variant 0.12 ethambutol
embC 4240803 p.Tyr314Phe missense_variant 0.13 ethambutol
embC 4241673 p.Ala604Gly missense_variant 1.0 ethambutol 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 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R