TB-Profiler result

Run: ERR7363097
Summary

Run ID: ERR7363097

Sample name:

Date: 2024-10-04T12:10:50.909891

Number of reads: 2339719

Percentage reads mapped: 99.66

Median coverage: 64.0

Strain: lineage4.3.4.2;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 0.1
lineage4.4.1 Euro-American (S-type) None 0.89
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.89
lineage4.3.4 Euro-American (LAM) RD174 0.11
lineage4.3.4.2 Euro-American (LAM) RD174 0.12
lineage4.4 Euro-American None 0.89
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 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.98 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13428 p.Ala44Glu missense_variant 0.17 isoniazid Uncertain significance
mshA 576108 p.Ala254Gly missense_variant 0.29 isoniazid
ethionamide
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
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 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.75 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.85 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
folC 2747605 c.-7C>G upstream_gene_variant 0.82 para-aminosalicylic_acid
Rv2477c 2783675 p.Gly123Asp missense_variant 0.89 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
pepQ 2860518 c.-100C>T upstream_gene_variant 0.16 bedaquiline
clofazimine
thyA 3073868 p.Thr202Ala missense_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.95 ethionamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.19 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.9 pyrazinamide Not assoc w R
Rv3236c 3612737 p.Ile127Thr missense_variant 0.15 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.5 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.92 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243577 c.345C>T synonymous_variant 0.95 ethambutol Not assoc w R - Interim
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 0.21 streptomycin Not assoc w R