TB-Profiler result

Run: SRR7131008
Summary

Run ID: SRR7131008

Sample name:

Date: 2024-10-05T09:12:55.934653

Number of reads: 1638081

Percentage reads mapped: 99.99

Median coverage: 56.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 0.91
lineage4 Euro-American None 0.95
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Phe81Val Uncertain significance Mutation from literature
streptomycin gid c.575delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine ald c.464delG Mutation from literature
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 761155 p.Ser450Leu missense_variant 0.96 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid Assoc w R High-level resistance
pncA 2289001 p.Phe81Val missense_variant 0.87 pyrazinamide Uncertain significance Mutation from literature
ald 3087278 c.464delG frameshift_variant 0.9 cycloserine Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.95 ethambutol Uncertain significance Mutation from literature
gid 4407627 c.575delG frameshift_variant 0.95 streptomycin 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
nusG 733867 c.-386_-381delGCGGTC upstream_gene_variant 0.9 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.95 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.81 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
pncA 2289047 c.195C>T synonymous_variant 0.1 pyrazinamide Not assoc w R
Rv2681 2997436 p.Arg233Pro missense_variant 0.96 capreomycin Uncertain significance
mtrA 3627595 c.-246G>A upstream_gene_variant 0.93 rifampicin Uncertain significance
bedaquiline Uncertain significance
clpC1 4039889 c.816G>A synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.98 ethambutol Not assoc w R
ethR 4327826 p.Asn93Ser missense_variant 0.95 ethionamide 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