TB-Profiler result

Run: SRR13837544
Summary

Run ID: SRR13837544

Sample name:

Date: 2024-10-04T02:22:43.723200

Number of reads: 597151

Percentage reads mapped: 96.55

Median coverage: 20.0

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
dnaA 1110 c.1110T>G synonymous_variant 1.0 isoniazid
gyrB 5760 p.Trp174Leu missense_variant 1.0 levofloxacin
moxifloxacin
gyrB 6662 p.Phe475Val missense_variant 1.0 levofloxacin
moxifloxacin Uncertain significance
rpoB 760087 p.Ser94Phe missense_variant 0.94 rifampicin
rpoC 766854 p.Leu1162Gln missense_variant 1.0 rifampicin
mmpL5 778416 p.Pro22Leu missense_variant 1.0 bedaquiline
clofazimine
rplC 801126 c.318C>T synonymous_variant 1.0 linezolid
Rv1129c 1254196 c.338delT frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
sigE 1364560 p.His50Asn missense_variant 1.0 pyrazinamide
rrl 1475354 n.1697A>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid Uncertain significance
inhA 1674867 p.Trp222Cys missense_variant 0.88 isoniazid
ethionamide
katG 2154601 p.Gly504Val missense_variant 1.0 isoniazid
Rv1979c 2222910 c.255A>G synonymous_variant 1.0 bedaquiline
clofazimine
pepQ 2859714 c.705C>A synonymous_variant 1.0 bedaquiline
clofazimine
Rv2752c 3066476 c.-285C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3087172 p.Glu118Ala missense_variant 1.0 cycloserine
ald 3087905 c.1086G>A synonymous_variant 1.0 cycloserine
Rv3236c 3613280 c.-164G>C upstream_gene_variant 1.0 pyrazinamide
Rv3236c 3613355 c.-239C>G upstream_gene_variant 1.0 pyrazinamide
lpqB 3623494 p.Ala473Pro missense_variant 0.96 rifampicin
bedaquiline
lpqB 3624600 p.Val104Gly missense_variant 1.0 rifampicin
bedaquiline
lpqB 3624838 p.Pro25Ser missense_variant 1.0 rifampicin
bedaquiline
alr 3841499 c.-79C>T upstream_gene_variant 1.0 cycloserine
rpoA 3878156 p.Val118Met missense_variant 0.96 rifampicin
clpC1 4039113 p.Ala531Asp missense_variant 0.85 pyrazinamide
glpK 4139244 p.Ala171Gly missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242095 p.Ala745Pro missense_variant 1.0 ethambutol
embB 4247621 c.1108C>T synonymous_variant 0.95 ethambutol
ubiA 4269585 c.249G>A synonymous_variant 0.95 ethambutol Not assoc w R - Interim
ubiA 4269776 p.Ala20Pro missense_variant 1.0 ethambutol
ethA 4328211 c.-739delG upstream_gene_variant 1.0 ethionamide