Advanced Strain Search

Penvy-Col4-PS

PSP 10043

DNA Source: Premium Spores

General Information

Accession Date
May 11, 2021
Report Type
Whole-Genome Sequencing
DNA Source Website
premiumspores.com

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 51 of 110 cultivars (47th percentile).

Clonal or not?

Assessing…

Interactive 3D Psilocybe Atlas See Penvy-Col4-PS in the tree of life Spin, zoom, and explore exactly where Penvy-Col4-PS sits among its closest genetic relatives. Launch 3D tree

Clone Test

Is Penvy-Col4-PS 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 Penvy-Col4-PS 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.

psiH 1 variant — 1 MODERATE
psiH
MODERATE I17V p.Ile17Val missense A/G Reads only
chr10:1667559 2 of 11 reads

Genetic Relatives

Nearest

  1. Penvy-1-PS (PSP10045) — 0.001
  2. Penvy-Col5-PS (PSP10044) — 0.001
  3. Penvy-2-SW (PSP10075) — 0.002
  4. Orissa-India-1-Mush (PSP10072) — 0.173
  5. Orissa-India-4-Mush (PSP10073) — 0.192
  6. Costa-Rica-1-redo-SW (PSP10022) — 0.271
  7. Costa-Rica-2-redo-SW (PSP10023) — 0.272
  8. Costa-Rica-3-redo-SW (PSP10024) — 0.296
  9. Treasure-Coast-2-Mush (PSP10082) — 0.315
  10. Treasure-coast-3-PS (PSP10056) — 0.316
  11. Treasure-coast-1-PS (PSP10054) — 0.316
  12. Treasure-coast-2-PS (PSP10055) — 0.317
  13. Bplus-ITW-WM (PSP10129) — 0.317
  14. Roatan-Honduras-4-Mush (PSP10079) — 0.321
  15. Tosohatchee-print-ITW (PSP10081) — 0.326
  16. Arenal-Volcano-1-Mush (PSP10059) — 0.328
  17. MGC_2016_unknown_strain (PSP10012) — 0.332
  18. ColumbiaRust-1-SW (PSP10021) — 0.333
  19. Z-strain-1-Mush (PSP10083) — 0.334
  20. Costa-Rica-1-redo-SW (PSP10003) — 0.335

Most Distant

  1. Bplus-3-PS (PSP10001) — 0.728
  2. GoldenCoast-BAF-B1-UM (PSP10107) — 0.725
  3. GoldenCoast-BAF-A1-UM (PSP10105) — 0.724
  4. GoldenCoast-BAF-B2-UM (PSP10108) — 0.724
  5. Maui-2-PS (PSP10041) — 0.722
  6. Orissa-India-ITW (PSP10071) — 0.722
  7. GoldenCoast-BAF-A2-UM (PSP10106) — 0.722
  8. Huautla-3-PS (PSP10005) — 0.722
  9. Huautla-2-redo-SW (PSP10030) — 0.721
  10. GoldenTeacher-3-SW (PSP10029) — 0.721
  11. Huautla-3-redo-SW (PSP10031) — 0.721
  12. Ecuador-3-SW (PSP10025) — 0.721
  13. Bplus-2-redo-SW (PSP10015) — 0.721
  14. Maui-1-PS (PSP10040) — 0.720
  15. Maui-3-PS (PSP10042) — 0.720
  16. Bplus-1-redo-SW (PSP10014) — 0.720
  17. Bplus-3-redo-SW (PSP10016) — 0.718
  18. Puerto-Rican-ITW (PSP10078) — 0.717
  19. Gulf-Coast (PSP10091) — 0.717
  20. Gulf-Coast-BAF (PSP10090) — 0.717

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 Penvy-Col4-PS 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
5239c45abf594bb7af860aad4a52965e33a732ed7c59bed5633074bd1f9a5384
Stamping Certificate
Download PDF (39.4 KB)
SHASUM Hash
2c228eda6710472694cde753cd41306f4ddca84ed1dc0e0f654c31d002a0535f

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