TB-Profiler result

Run: ERR108464

Summary

Run ID: ERR108464

Sample name:

Date: 2024-03-25T20:18:18.568473

Number of reads: 4624684

Percentage reads mapped: 99.44

Median coverage: 99.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: HR-TB


Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.83
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.19
lineage4.2.1 Euro-American (TUR) None 0.84
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.86 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.89 isoniazid Assoc w R High-level resistance
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 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13441 p.Thr40Pro missense_variant 0.16 isoniazid Uncertain significance
Rv0010c 13454 c.105C>T synonymous_variant 0.14 isoniazid 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 0.8 linezolid
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.18 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.12 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.8 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 0.83 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 0.84 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.19 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.89 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.12 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.9 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.89 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.92 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625403 p.Val404Ala missense_variant 0.85 bedaquiline Uncertain significance
rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249354 c.2841G>C synonymous_variant 0.21 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.79 ethambutol Not assoc w R - Interim
ethR 4327937 p.Thr130Ile missense_variant 0.16 ethionamide
ethA 4328376 c.-903G>C upstream_gene_variant 0.87 ethionamide
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 4338598 c.-77G>C upstream_gene_variant 0.11 capreomycin
amikacin Uncertain significance
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 0.92 capreomycin
amikacin
kanamycin