TB-Profiler result

Run: ERR4820334

Summary

Run ID: ERR4820334

Sample name:

Date: 20-10-2023 09:19:32

Number of reads: 3328336

Percentage reads mapped: 96.76

Strain: lineage4.4.1.1

Drug-resistance: Other


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
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.36)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.36 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.4
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.48
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.48
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.65
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.54
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.58
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.64
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.59
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.4
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.43
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.73
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.73
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.72
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.78
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.73
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.87
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.76
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.72
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.47
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.38
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.35
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.65
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.65
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.65
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.74
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.71
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.74
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.73
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.64
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.52
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.52
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.62
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.52
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.55
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.58
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.52
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.48
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.37
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.44
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.56
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.56
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.55
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.61
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.59
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.66
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.61
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.57
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.57
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.61
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.45
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.36
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.65
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.7
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0