TB-Profiler result

Run: SRR1222721
Summary

Run ID: SRR1222721

Sample name:

Date: 2024-05-17T15:35:31.477330

Number of reads: 2890148

Percentage reads mapped: 92.59

Median coverage: 18.0

Strain: lineage4.1.2.1;lineage4.2.1;lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.18
lineage4.1.2 Euro-American None 0.17
lineage4.2 Euro-American None 0.65
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.14
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.56
lineage4.9 Euro-American (H37Rv-like) None 0.49
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 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.42 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
capreomycin
rrl 1475145 n.1488C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674102 c.-100C>A upstream_gene_variant 0.71 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.96 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.56 isoniazid
embB 4249594 c.3081G>A synonymous_variant 0.71 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.64 ethionamide
gid 4408027 p.Leu59Arg missense_variant 0.65 streptomycin Uncertain significance