TB-Profiler result

Run: ERR11465175
Summary

Run ID: ERR11465175

Sample name:

Date: 2024-10-04T01:08:09.941448

Number of reads: 6156212

Percentage reads mapped: 99.64

Median coverage: 172.0

Strain: lineage4.3.4.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.52
lineage4.3.4.1 Euro-American (LAM) RD174 0.57
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.46
lineage4.3.4 Euro-American (LAM) RD174 0.54
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 1465 p.Glu489Lys missense_variant 0.46 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.52 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 0.55 isoniazid Uncertain significance
mshA 576574 c.1227T>C synonymous_variant 0.54 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.52 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777128 c.1353A>G synonymous_variant 0.1 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.57 pyrazinamide 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 0.45 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.45 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.32 pyrazinamide Not assoc w R
Rv1979c 2222854 p.Ile104Thr missense_variant 0.54 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.53 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.6 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.48 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.6 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.65 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877884 c.624G>A synonymous_variant 0.46 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.6 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 0.53 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 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
whiB6 4338732 c.-211C>T upstream_gene_variant 0.53 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.45 streptomycin Not assoc w R