TB-Profiler result

Run: ERR4818208

Summary

Run ID: ERR4818208

Sample name:

Date: 20-10-2023 08:36:44

Number of reads: 1272202

Percentage reads mapped: 97.67

Strain: lineage4.1.1.3.1

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.50)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 0.99
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.5 streptomycin
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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
fbiC 1303601 p.Glu224Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.53
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.37
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.33
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.35
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.55
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.52
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.58
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.65
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.57
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.57
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.57
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.57
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.57
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.56
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.56
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.38
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.38
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0