TB-Profiler result

Run: ERR2184621
Summary

Run ID: ERR2184621

Sample name:

Date: 2024-10-03T17:36:10.819434

Number of reads: 2961785

Percentage reads mapped: 99.67

Median coverage: 106.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.95
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 gyrB p.Arg446Cys Uncertain significance Mutation from literature
gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Arg446Cys Uncertain significance Mutation from literature
gyrA p.Ser91Pro Assoc w R
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
gyrB 6575 p.Arg446Cys missense_variant 0.15 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7572 p.Ser91Pro missense_variant 0.66 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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 9217 p.Asp639Gly missense_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.93 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 767302 c.3933C>T synonymous_variant 0.95 rifampicin Not assoc w R - Interim
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.88 capreomycin Not assoc w R
linezolid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.96 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
pepQ 2860283 p.Phe46Leu missense_variant 0.93 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.94 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.95 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.94 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.97 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R