TB-Profiler result

Run: ERR11465563
Summary

Run ID: ERR11465563

Sample name:

Date: 03-01-2024 05:58:06

Number of reads: 865737

Percentage reads mapped: 99.24

Strain: lineage4.1.2.1

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 (0.23), rrs n.1484G>T (0.16)
Amikacin R rrs n.1402C>A (0.23), rrs n.1484G>T (0.16)
Capreomycin R rrs n.1402C>A (0.23), rrs n.1484G>T (0.16)
Kanamycin R rrs n.1402C>A (0.23), rrs n.1484G>T (0.16)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.97
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 0.23 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.16 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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763589 p.Ile74Val missense_variant 0.2
rpoC 764470 c.1101C>G synonymous_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val 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 1472380 n.535G>C non_coding_transcript_exon_variant 0.24
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.28
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.36
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.26
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.16
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.18
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.22
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.24
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.16
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rpsA 1833959 p.Leu140Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746195 c.1404C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0