TB-Profiler result

Run: ERR4818465
Summary

Run ID: ERR4818465

Sample name:

Date: 20-10-2023 08:40:40

Number of reads: 7768727

Percentage reads mapped: 94.73

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.888G>A (0.82)
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.82 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
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 1.0
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 1472106 n.261G>A non_coding_transcript_exon_variant 0.17
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.16
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.18
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.18
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.18
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.18
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.2
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.68
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.7
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.77
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.77
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.7
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.82
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.59
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.59
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.82
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.84
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.83
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.78
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.91
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.9
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.81
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.89
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.87
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.84
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.59
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.38
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.38
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.18
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.17
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.13
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.23
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.21
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.22
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.32
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.28
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102198 p.Ala282Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169965 c.648C>T synonymous_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 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240009 c.147G>A synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0