TB-Profiler result

Run: ERR11465468
Summary

Run ID: ERR11465468

Sample name:

Date: 2024-10-05T03:58:52.476362

Number of reads: 5713126

Percentage reads mapped: 99.64

Median coverage: 137.0

Strain: lineage4.3.4.2.1;lineage4.4.1.1

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 0.68
lineage4.4.1 Euro-American (S-type) None 0.3
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.32
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.69
lineage4.3.4 Euro-American (LAM) RD174 0.7
lineage4.3.4.2 Euro-American (LAM) RD174 0.69
lineage4.4 Euro-American None 0.33
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 6140 p.Val301Leu missense_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.63 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 777416 c.1065G>T synonymous_variant 0.34 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
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917738 c.-202G>A upstream_gene_variant 0.21 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.29 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2155953 c.159C>G synonymous_variant 0.77 isoniazid Not assoc w R - Interim
katG 2155987 p.Arg42Pro missense_variant 0.28 isoniazid
PPE35 2168479 p.Thr712Pro missense_variant 0.28 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.31 pyrazinamide 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
thyA 3073868 p.Thr202Ala missense_variant 0.71 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.32 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Not assoc w R
Rv3236c 3612009 p.Ala370Thr missense_variant 0.73 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.22 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.79 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.71 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.27 ethambutol 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 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.69 streptomycin Not assoc w R