TB-Profiler result

Run: ERR4820922
Summary

Run ID: ERR4820922

Sample name:

Date: 20-10-2023 09:29:55

Number of reads: 6078894

Percentage reads mapped: 96.39

Strain: lineage4.1.2.1

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 (0.56)
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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.56 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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_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 1.0
rrs 1471649 n.-197C>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.32
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.54
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.53
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.6
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.62
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.68
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.64
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.69
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.77
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.79
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.46
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.46
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.59
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.57
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.48
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.47
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.47
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.38
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.38
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.5
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.45
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.45
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.56
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.35
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.61
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.6
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.76
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.64
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.79
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.75
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.82
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.75
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.77
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.7
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.59
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.52
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.48
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.35
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.35
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.48
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.57
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.61
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.65
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.68
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.59
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.69
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.77
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.66
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.6
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.6
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.73
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.73
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.73
rrl 1475760 n.2103_2107delCCGCAinsACCCCCCG non_coding_transcript_exon_variant 0.67
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.67
rrl 1475767 n.2110_2111insT non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.69
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.5
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.62
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.62
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.62
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.71
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.84
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.73
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338676 c.-155T>C upstream_gene_variant 1.0