TB-Profiler result

Run: ERR4815837
Summary

Run ID: ERR4815837

Sample name:

Date: 20-10-2023 07:56:16

Number of reads: 2610376

Percentage reads mapped: 92.39

Strain: lineage4.1.4

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 rpsL p.Lys88Arg (1.00), rrs n.888G>A (0.96)
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
lineage4.1.4 Euro-American T;X;H 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
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.96 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
mmpL5 778042 p.Ala147Thr 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 1472530 n.685G>A non_coding_transcript_exon_variant 0.89
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.91
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.91
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.91
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.87
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.8
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.93
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.87
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.87
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.93
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.93
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.96
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.96
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.96
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.96
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.91
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.78
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.81
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.41
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.41
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.44
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.57
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.57
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.56
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.67
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.67
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.67
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 0.6
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.46
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.44
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.55
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.57
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.59
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0