TB-Profiler result

Run: ERR4821731

Summary

Run ID: ERR4821731

Sample name:

Date: 20-10-2023 09:43:06

Number of reads: 3640974

Percentage reads mapped: 98.11

Strain: 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.799C>T (0.75)
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 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.75 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 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile 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 1472150 n.305T>A non_coding_transcript_exon_variant 0.71
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.83
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.83
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.86
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.86
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.86
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.8
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.79
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.86
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.87
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.81
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.73
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.89
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.89
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.89
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.89
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.91
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.89
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.89
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.89
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.88
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.84
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.85
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.84
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.8
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.73
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.7
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.69
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.69
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.69
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.69
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.71
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.7
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.66
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.62
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.87
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.93
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.9
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.9
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A 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
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0