TB-Profiler result

Run: SRR6046818

Summary

Run ID: SRR6046818

Sample name:

Date: 20-10-2023 18:08:34

Number of reads: 1707534

Percentage reads mapped: 90.4

Strain: lineage4.2.1

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 (0.37)
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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 0.37 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 765248 c.1879T>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779275 p.Arg96Gly 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 1472566 n.721G>A non_coding_transcript_exon_variant 0.46
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.48
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.27
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.46
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.46
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.53
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.36
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.27
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.41
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.35
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.37
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.38
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.36
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.39
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.56
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.6
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.57
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.53
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.45
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.45
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.42
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.39
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.46
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.44
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.38
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.38
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.38
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.33
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.33
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.43
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.47
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.47
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.49
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.61
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.54
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.32
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.97
Rv1979c 2223284 c.-120C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 0.99
gid 4408149 c.54T>C synonymous_variant 1.0