TB-Profiler result

Run: ERR4817526

Summary

Run ID: ERR4817526

Sample name:

Date: 20-10-2023 08:25:01

Number of reads: 1573911

Percentage reads mapped: 90.39

Strain: lineage4.4.1.1

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 (0.48)
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
lineage4.4 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.48 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 1472124 n.279C>T non_coding_transcript_exon_variant 0.62
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.75
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.42
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.41
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.58
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.39
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.79
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.57
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.69
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.44
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.6
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.87
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.83
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.86
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.93
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.87
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.92
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.85
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.88
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.88
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.85
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.83
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.83
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.71
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.67
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.71
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.75
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.53
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.62
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.54
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.54
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.9
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.9
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.91
rrl 1474734 n.1077G>C non_coding_transcript_exon_variant 0.9
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.82
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.8
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.82
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.82
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.91
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.8
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.91
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.72
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.28
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.65
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