TB-Profiler result

Run: ERR2229148

Summary

Run ID: ERR2229148

Sample name:

Date: 20-10-2023 20:51:23

Number of reads: 1515050

Percentage reads mapped: 94.83

Strain: lineage4.8

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
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1402C>A (0.16)
Amikacin R rrs n.1402C>A (0.16)
Capreomycin R rrs n.1402C>A (0.16)
Kanamycin R rrs n.1402C>A (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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.16 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
rpoC 763642 c.273G>C synonymous_variant 0.13
rpoC 763660 c.291T>G synonymous_variant 0.16
rpoC 763661 p.Ala98Arg missense_variant 0.12
rpoC 763666 c.297G>C synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.13
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.19
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.16
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.16
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.23
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.21
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.16
rrs 1472675 n.830T>G non_coding_transcript_exon_variant 0.17
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.2
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.19
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.19
rrs 1472685 n.840G>T non_coding_transcript_exon_variant 0.16
rrs 1472701 n.856T>C non_coding_transcript_exon_variant 0.22
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.14
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.17
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.41
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.13
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.16
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.18
rrl 1475743 n.2086T>C non_coding_transcript_exon_variant 0.21
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.17
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.19
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.21
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.2
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.2
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.17
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>A non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0