TB-Profiler result

Run: SRR6046219
Summary

Run ID: SRR6046219

Sample name:

Date: 20-10-2023 18:14:57

Number of reads: 2240543

Percentage reads mapped: 91.82

Strain: lineage4.8;lineage3

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 (0.43)
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
lineage3 East-African-Indian CAS RD750 0.4
lineage4 Euro-American LAM;T;S;X;H None 0.66
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.62
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 0.43 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 0.32
gyrA 9304 p.Gly668Asp missense_variant 0.55
fgd1 491742 c.960T>C synonymous_variant 0.24
rpoB 759746 c.-61C>T upstream_gene_variant 0.42
rpoC 762434 c.-936T>G upstream_gene_variant 0.44
rpoC 763031 c.-339T>C upstream_gene_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303331 p.Arg134Gln missense_variant 0.39
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.47
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.45
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.52
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.44
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.56
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.53
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.41
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.5
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.46
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.38
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.41
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.46
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.43
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.38
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.36
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.32
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.21
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.39
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.26
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.55
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.58
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.89
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.63
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.71
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.39
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.49
PPE35 2167926 p.Leu896Ser missense_variant 0.45
PPE35 2169308 c.1305C>T synonymous_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.34
pncA 2289365 c.-125delC upstream_gene_variant 0.43
pncA 2289799 c.-558G>A upstream_gene_variant 0.52
ahpC 2726105 c.-88G>A upstream_gene_variant 0.39
ald 3086788 c.-32T>C upstream_gene_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.25
fprA 3474893 p.Ser296Cys missense_variant 0.38
Rv3236c 3612390 p.Gly243Ser missense_variant 0.79
embC 4242075 p.Arg738Gln missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246729 c.216C>T synonymous_variant 0.65
whiB6 4338469 p.Asn18Thr missense_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.31