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GoldenCoast-UM

PSP 10109

DNA Source: USA Mycology & More

General Information

Accession Date
June 1, 2022
Report Type
Whole-Genome Sequencing

This visualization shows how genetically distinctive this sample is compared to every other sample in this database. Distinctiveness is the average genetic distance from this sample to its five nearest samples: a sample with no close relatives in the collection scores high (rare), while one with several near-identical samples, for example repeated submissions of the same cultivar, scores low (common). The curve is the distribution of that score across the whole collection and the marker shows where this sample falls, so you can read, as a single percentile, how unique it is within this database rather than just how far it is from its nearest match.

Rarity: Common

More genetically distinct than 34 of 110 cultivars (31st percentile).

Clonal or not?

Assessing…

Interactive 3D Psilocybe Atlas See GoldenCoast-UM in the tree of life Spin, zoom, and explore exactly where GoldenCoast-UM sits among its closest genetic relatives. Launch 3D tree

Clone Test

Is GoldenCoast-UM a resequencing of a culture already in Psilocydia? Every assembled genome was aligned directly to its closest genome in the collection and the divergence measured. Pairs that are one culture sequenced twice sit at or below about 0.03%; genuinely different cultures sit well above it. Where GoldenCoast-UM falls on that scale answers the question, calibrated against the collection's own resequencings rather than a rule of thumb.

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Genetic Information

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What is in the assembly

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Variants

Changes in the psilocybin genes were found by two independent analysis methods applied to this sample's sequencing reads: aligning the reads to the reference genome, and assembling the genome from them. Each change is labelled with the method that found it, or Both; hover a label for the read counts.

How we found these
Both
In the assembly and in the reads, so confirmed twice.
Reads only
In the reads, not in the assembly. The hover says why where we know: the assembly has the reference base there, does not cover the site, or this sample has no assembly. Many of these are changes carried by only part of the reads; an assembly keeps one base at each position.
Assembly only
In the assembly, but the reads show the reference base there, or too few reads cover the site to say.

Read counts. At every site we count the reads carrying each base (reads with mapping quality of at least 20, bases with quality of at least 13; 8 reads or more to say anything). The change is in most reads at 80% or more, mixed between 20% and 80%, in a minority from 5% to 20% (and at least 2 reads), and essentially absent below that. These counts say what the reads show; they say nothing about how many copies of the gene the sample carries. A change counts as found in the reads when these counts show it (in most, mixed or a minority of reads) or when the lab's variant report lists it. That report lists only changes its gene models rate HIGH or MODERATE, so many changes the reads show are not on it.

Names. Protein changes are named on our curated gene models for the psilocybin cluster. The read-alignment report names them on the public reference's gene models, which in places differ (for example, the public models join psiT1 and psiK into one gene); where the names differ, the hover shows both.

What is listed. Changes that alter the protein (rated HIGH or MODERATE), and every change on the lab's variant report for the cluster. Positions are on chromosome 10 of the reference genome.

psiT1 2 variants — 2 MODERATE
psiT1
MODERATE E121G p.Glu121Gly missense A/G Assembly only
chr10:1663786 7 of 7 reads
psiT1
MODERATE I214L p.Ile214Leu missense A/C Both
chr10:1664184 14 of 14 reads
psiK 1 variant — 1 MODERATE
psiK
MODERATE R173G p.Arg173Gly missense A/G Both
chr10:1666622 23 of 23 reads
psiH 4 variants — 4 MODERATE
psiH
MODERATE S7F p.Ser7Phe missense C/T Both
chr10:1667530 13 of 13 reads
psiH
MODERATE 115GF>115G inframe deletion GTTC/G Reads only
chr10:1667959 2 of 9 reads
psiH
MODERATE T502S p.Thr502Ser missense A/T Both
chr10:1669642 19 of 19 reads
psiH
MODERATE L508P p.Leu508Pro missense T/C Both
chr10:1669661 17 of 17 reads
psiM 1 variant — 1 MODERATE
psiM
MODERATE R102K p.Arg102Lys missense C/T Both
chr10:1674573 17 of 17 reads
psiD 3 variants — 3 MODERATE
psiD
MODERATE Q253K p.Gln253Lys missense G/T Reads only
chr10:1676745 4 of 23 reads
psiD
MODERATE G206N p.Gly206Asn missense CC/TT Both
chr10:1676885 18 of 18 reads
psiD
MODERATE L22F p.Leu22Phe missense C/A Both
chr10:1677485 23 of 23 reads

Genetic Relatives

Nearest

  1. GoldenTeacher-3-SW (PSP10029) — 0.052
  2. Ecuador-3-SW (PSP10025) — 0.053
  3. Maui-2-PS (PSP10041) — 0.054
  4. Maui-1-PS (PSP10040) — 0.056
  5. Maui-3-PS (PSP10042) — 0.056
  6. GoldenTeacher-2-SW (PSP10028) — 0.056
  7. Ecuador-3-PS (PSP10061) — 0.057
  8. Golden-Teacher (PSP10089) — 0.058
  9. GoldenTeacher-1-SW (PSP10027) — 0.058
  10. Bplus-2-redo-SW (PSP10015) — 0.061
  11. Bplus-1-redo-SW (PSP10014) — 0.061
  12. Bplus (PSP10088) — 0.061
  13. Bplus-3-redo-SW (PSP10016) — 0.061
  14. Huautla-3-PS (PSP10005) — 0.063
  15. HUA-Early (PSP10092) — 0.064
  16. Huautla-3-redo-SW (PSP10031) — 0.064
  17. Huautla-2-redo-SW (PSP10030) — 0.065
  18. Z-strain-3-PS (PSP10084) — 0.065
  19. PES-2-SW (PSP10008) — 0.066
  20. Bplus-3-PS (PSP10001) — 0.068

Most Distant

  1. Penvy-1-PS (PSP10045) — 0.703
  2. Penvy-Col5-PS (PSP10044) — 0.703
  3. Penvy-Col4-PS (PSP10043) — 0.703
  4. Penvy-2-SW (PSP10075) — 0.702
  5. Costa-Rica-1-redo-SW (PSP10022) — 0.653
  6. Treasure-coast-1-PS (PSP10054) — 0.651
  7. Treasure-coast-3-PS (PSP10056) — 0.650
  8. Treasure-coast-2-PS (PSP10055) — 0.650
  9. Treasure-Coast-2-Mush (PSP10082) — 0.649
  10. Costa-Rica-2-redo-SW (PSP10023) — 0.649
  11. Costa-Rica-3-redo-SW (PSP10024) — 0.622
  12. Bplus-ITW-WM (PSP10129) — 0.611
  13. Arenal-Volcano-1-Mush (PSP10059) — 0.606
  14. Luminous-lucies-2-PS (PSP10032) — 0.602
  15. Luminous-lucies-3-PS (PSP10033) — 0.602
  16. Luminous-lucies-1-PS (PSP10034) — 0.602
  17. Orissa-India-1-Mush (PSP10072) — 0.601
  18. Roatan-Honduras-4-Mush (PSP10079) — 0.601
  19. Orissa-India-4-Mush (PSP10073) — 0.601
  20. ColumbiaRust-1-SW (PSP10021) — 0.600

Sequence Data Downloads

The blockchain-registered VCF above can be downloaded by anyone, so its hash can be checked independently against the blockchain record. The remaining sequence data files — FASTQ, BAM and assemblies — are available to authorised accounts. Log in to download, or contact us for access.

Psilocybin

The psilocybin biosynthesis genes sit together in one cluster on chromosome 10 (psiD, psiK, psiM, psiH, psiR, psiT1, psiT2). Every assembled genome in Psilocydia was compared with the MGC_Penvy_1 reference across this window; below are the variants GoldenCoast-UM carries there, and which other samples carry the same ones. This section compares assemblies only; the psilocybin gene cards under Variants combine the assembly with the reads, so they can list changes that are not here.

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The enzymes in 3D

This sample's version of each enzyme next to the P. Envy reference's. Flip between the two models; the track underneath shows every change seen in the collection and how many samples carry it, with this sample's changes filled in.

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Blockchain Registration Information

Transaction ID
bb204ee5beefa05011072c6d0ac2913314cf15e26a7c7fd41ca62c7267eb299b
Stamping Certificate
Download PDF (39.6 KB)
SHASUM Hash
b070d338f30057ae0d2f275852077c3f6fb195c7f3e2a1c70e1d083483ada818

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