TB-Profiler result

Run: ERR4811541
Summary

Run ID: ERR4811541

Sample name:

Date: 2024-04-15T18:52:01.132301

Number of reads: 6272843

Percentage reads mapped: 99.56

Median coverage: 180.0

Strain: lineage4.2.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.32
lineage4.5 Euro-American RD122 0.66
lineage4.2 Euro-American None 0.31
lineage4 Euro-American None 1.0
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
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 7892 c.591G>A synonymous_variant 0.68 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7946 c.645C>T synonymous_variant 0.36 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13394 p.Trp55* stop_gained 0.69 isoniazid Uncertain significance
Rv0010c 13630 c.-72G>A upstream_gene_variant 0.12 isoniazid Uncertain significance
mshA 576077 c.730C>T synonymous_variant 0.26 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.68 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.29 linezolid
Rv1129c 1254129 p.Gly136Ser missense_variant 0.65 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254591 c.-57C>T upstream_gene_variant 0.66 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
tlyA 1918605 c.666C>T synonymous_variant 0.31 capreomycin
bacA 2063685 c.1044G>A synonymous_variant 0.31 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.7 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726004 c.-189G>C upstream_gene_variant 0.32 isoniazid
Rv2752c 3065534 p.Pro220Thr missense_variant 0.65 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.28 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.36 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.39 cycloserine
Rv3236c 3612469 c.648A>G synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
Rv3236c 3612992 p.Ser42Gln missense_variant 0.72 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878575 c.-68C>T upstream_gene_variant 0.69 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 0.65 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.67 pyrazinamide Not assoc w R
embC 4242201 p.Gly780Asp missense_variant 0.33 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin