TB-Profiler result

Run: ERR4821291

Summary

Run ID: ERR4821291

Sample name:

Date: 20-10-2023 09:35:55

Number of reads: 3079170

Percentage reads mapped: 98.54

Strain: lineage4.2.1.1

Drug-resistance: HR-TB


Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide R pncA p.Tyr95* (1.00)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.His22Pro (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 1.0
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288957 p.Tyr95* stop_gained 1.0 pyrazinamide
ethA 4327409 p.His22Pro missense_variant 1.0 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575833 c.486C>T synonymous_variant 1.0
mshA 576092 p.Pro249Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800973 c.165C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471755 n.-91C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.47
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.47
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.53
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.6
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.54
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.6
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.57
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.57
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.58
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.58
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449132 p.Leu210Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987092 p.Glu83Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246587 p.Gly25Ala missense_variant 1.0
embB 4247790 p.Ser426Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407969 c.233dupC frameshift_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0