TB-Profiler result

Run: ERR182046

Summary

Run ID: ERR182046

Sample name:

Date: 20-10-2023 22:41:43

Number of reads: 3016359

Percentage reads mapped: 97.56

Strain: lineage4.3.4.2.1

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 (0.12)
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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 0.12 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767083 c.3714C>T synonymous_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 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.16
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.21
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.21
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.1
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.14
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.13
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.14
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.15
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.15
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.1
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.24
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.24
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.28
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.2
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.16
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.15
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.15
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.15
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.15
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.14
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840869 c.552C>G synonymous_variant 0.98
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240572 p.Gly237Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0