TB-Profiler result

Run: ERR4817840
Summary

Run ID: ERR4817840

Sample name:

Date: 20-10-2023 08:30:29

Number of reads: 3669606

Percentage reads mapped: 97.22

Strain: lineage3.1.2.2

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1402C>A (0.28)
Amikacin R rrs n.1402C>A (0.28)
Capreomycin R rrs n.1402C>A (0.28)
Kanamycin R rrs n.1402C>A (0.28)
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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.2 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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.28 kanamycin, capreomycin, aminoglycosides, amikacin
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
gyrA 9611 c.2310C>T synonymous_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 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.26
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.3
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.3
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.3
rrs 1473022 n.1177G>A non_coding_transcript_exon_variant 0.26
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.26
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.34
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.35
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.32
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.26
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.3
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.19
rrs 1473292 n.1447_1449delGGAinsTGGG non_coding_transcript_exon_variant 0.2
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.2
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.15
rrl 1474662 n.1005C>A non_coding_transcript_exon_variant 0.37
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.35
rrl 1475526 n.1869C>G non_coding_transcript_exon_variant 1.0
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.23
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.27
rpsA 1833685 c.144G>C synonymous_variant 0.12
rpsA 1833694 c.153G>C synonymous_variant 0.13
rpsA 1833697 c.156C>G synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu 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
ald 3087476 c.657C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326176 p.Glu433Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0