TB-Profiler result

Run: ERR11465154
Summary

Run ID: ERR11465154

Sample name:

Date: 2024-04-16T09:06:38.618031

Number of reads: 7704750

Percentage reads mapped: 99.58

Median coverage: 200.0

Strain: lineage4.1.2.1;lineage4.2.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.52
lineage4.1.2 Euro-American None 0.57
lineage4.2 Euro-American None 0.49
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.51
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 0.5
lineage4.2.1 Euro-American (TUR) None 0.48
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.49 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.54 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.42 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.46 rifampicin Not assoc w R
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 0.55 linezolid
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.51 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406600 c.740dupT frameshift_variant 0.46 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1406622 p.Leu240Arg missense_variant 0.48 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475579 n.1922G>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
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
bacA 2063685 c.1044G>A synonymous_variant 0.38 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 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169356 c.1257C>T synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
PPE35 2169879 p.Phe245Cys missense_variant 0.36 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.45 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.37 capreomycin
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.53 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3986801 c.-43G>A upstream_gene_variant 0.48 delamanid
pretomanid
embC 4239298 c.-565C>T upstream_gene_variant 0.44 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.47 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