TB-Profiler result

Run: ERR11044261
Summary

Run ID: ERR11044261

Sample name:

Date: 2024-10-05T13:20:43.467094

Number of reads: 2638315

Percentage reads mapped: 99.67

Median coverage: 67.0

Strain: lineage4.7;lineage4.8

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 0.84
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.13
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 c.470delA Assoc w R High-level resistance
c.18dupA Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.89 streptomycin Assoc w R
katG 2155641 c.470delA frameshift_variant 0.73 isoniazid Assoc w R High-level resistance
katG 2156093 c.18dupA frameshift_variant 0.16 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
dnaA 1157 p.Asn386Ser missense_variant 0.25 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13807 c.-249G>A upstream_gene_variant 0.26 isoniazid
fgd1 491447 p.Val222Ala missense_variant 0.23 pretomanid
delamanid
clofazimine
rpoB 761823 p.Asn673His missense_variant 0.15 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775715 c.2766G>A synonymous_variant 0.88 bedaquiline Not assoc w R - Interim
clofazimine 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
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102006 p.Thr346Met missense_variant 0.87 isoniazid Uncertain significance
delamanid
ethionamide Uncertain significance
katG 2155437 p.Met225Ile missense_variant 0.17 isoniazid Uncertain significance
katG 2156207 c.-96T>G upstream_gene_variant 0.18 isoniazid
katG 2156703 c.-592C>T upstream_gene_variant 0.75 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726142 c.-51G>A upstream_gene_variant 0.82 isoniazid Uncertain significance
Rv2681 2997110 c.372G>A synonymous_variant 0.11 capreomycin Not assoc w R - Interim
Rv2752c 3065763 p.Tyr143* stop_gained 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.84 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407590 p.Ala205Thr missense_variant 0.86 streptomycin Uncertain significance
gid 4407967 p.Leu79Trp missense_variant 0.19 streptomycin Uncertain significance