TB-Profiler result

Run: ERR4816688
Summary

Run ID: ERR4816688

Sample name:

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

Number of reads: 1773909

Percentage reads mapped: 93.0

Strain: lineage4.2.2.2

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 (0.55)
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.78
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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 0.55 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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A 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 0.54
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.42
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.61
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.61
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.66
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.66
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.48
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.57
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.66
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.66
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.57
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.55
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.17
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.48
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.29
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.42
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.42
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.43
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.71
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.71
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.71
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.71
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.64
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.56
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067898 c.48C>T synonymous_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840746 p.Gln225His missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0