TB-Profiler result

Run: SRR13837696
Summary

Run ID: SRR13837696

Sample name:

Date: 2024-04-16T08:16:16.303534

Number of reads: 297264

Percentage reads mapped: 97.13

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.9 Euro-American (H37Rv-like) None 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
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
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
gyrB 6678 p.Pro480Arg missense_variant 1.0 levofloxacin
moxifloxacin
ccsA 620028 c.138G>C synonymous_variant 1.0 capreomycin
amikacin
kanamycin
rpoB 760454 c.650delG frameshift_variant 1.0 rifampicin
Rv1129c 1254452 p.Glu28Ala missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 0.93 streptomycin
kanamycin
capreomycin
amikacin
bacA 2063125 p.Ala535Asp missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2064843 c.-115C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
katG 2155857 c.255C>A synonymous_variant 1.0 isoniazid
thyA 3074067 c.405C>G synonymous_variant 0.94 para-aminosalicylic_acid
lpqB 3624738 p.Ala58Val missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625436 p.Ile393Asn missense_variant 1.0 bedaquiline
rifampicin
mtrA 3626728 p.Asp208Tyr missense_variant 1.0 bedaquiline
rifampicin
alr 3840223 c.1198A>C synonymous_variant 1.0 cycloserine
alr 3840711 p.Ser237Leu missense_variant 1.0 cycloserine
clpC1 4039648 p.Glu353Gln missense_variant 0.9 pyrazinamide
embC 4242023 p.Val721Leu missense_variant 1.0 ethambutol
ethA 4327364 p.Lys37Arg missense_variant 1.0 ethionamide