TB-Profiler result

Run: ERR031489
Summary

Run ID: ERR031489

Sample name:

Date: 2024-04-14T23:12:08.830836

Number of reads: 8278977

Percentage reads mapped: 99.58

Median coverage: 161.0

Strain: lineage4.3.4.2;lineage4.8

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 0.7
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.32
lineage4.3.4 Euro-American (LAM) RD174 0.68
lineage4.3.4.2 Euro-American (LAM) RD174 0.69
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 0.7 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8156 c.855T>G synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.29 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.7 rifampicin Not assoc w R
rpoC 767302 c.3933C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
mmpL5 775609 p.Ala958Thr missense_variant 0.31 clofazimine
bedaquiline
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.65 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.23 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
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.73 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.33 capreomycin
Rv2752c 3065293 p.Val300Ala missense_variant 0.58 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.77 para-aminosalicylic_acid
thyA 3074369 p.Arg35Cys missense_variant 0.26 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.8 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.69 pyrazinamide Not assoc w R
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.27 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.74 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.74 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.36 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.6 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239763 c.-100C>T upstream_gene_variant 0.73 ethambutol Not assoc w R
embC 4242083 c.2221C>T synonymous_variant 0.3 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.26 ethambutol Not assoc w R - Interim
whiB6 4338594 c.-73T>G upstream_gene_variant 0.16 capreomycin
amikacin
kanamycin
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 0.82 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.65 streptomycin Not assoc w R