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Puerto-Rican-ITW

PSP 10078

DNA Source: Inoculate the World

General Information

Accession Date
June 13, 2021
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 9 of 110 cultivars (8th percentile).

Clonal or not?

Assessing…

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

Clone Test

Is Puerto-Rican-ITW 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 Puerto-Rican-ITW 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 Both
chr10:1663786 50 of 50 reads
psiT1
MODERATE I214L p.Ile214Leu missense A/C Both
chr10:1664184 47 of 47 reads
between psiT1 and psiK 2 variants — 2 MODERATE
between psiT1 and psiK
MODERATE G>A outside the coding sequence G/A Both
chr10:1666040 48 of 48 reads
between psiT1 and psiK
MODERATE T>C outside the coding sequence T/C Both
chr10:1666041 48 of 48 reads
psiK 1 variant — 1 MODERATE
psiK
MODERATE R173G p.Arg173Gly missense A/G Both
chr10:1666622 56 of 56 reads
psiH 3 variants — 3 MODERATE
psiH
MODERATE S7F p.Ser7Phe missense C/T Both
chr10:1667530 32 of 32 reads
psiH
MODERATE T502S p.Thr502Ser missense A/T Both
chr10:1669642 39 of 39 reads
psiH
MODERATE L508P p.Leu508Pro missense T/C Both
chr10:1669661 34 of 34 reads
psiM 1 variant — 1 MODERATE
psiM
MODERATE R102K p.Arg102Lys missense C/T Both
chr10:1674573 32 of 32 reads
psiD 2 variants — 2 MODERATE
psiD
MODERATE G206N p.Gly206Asn missense CC/TT Both
chr10:1676885 33 of 33 reads
psiD
MODERATE L22F p.Leu22Phe missense C/A Both
chr10:1677485 72 of 72 reads

Genetic Relatives

Nearest

  1. GoldenCoast-BAF-B2-UM (PSP10108) — 0.043
  2. Huautla-3-PS (PSP10005) — 0.043
  3. GoldenCoast-BAF-B1-UM (PSP10107) — 0.044
  4. Gulf-Coast (PSP10091) — 0.045
  5. Gulf-Coast-BAF (PSP10090) — 0.046
  6. Bplus-2-redo-SW (PSP10015) — 0.047
  7. Huautla-3-redo-SW (PSP10031) — 0.047
  8. Bplus-1-redo-SW (PSP10014) — 0.047
  9. Golden-Teacher (PSP10089) — 0.048
  10. Bplus-3-redo-SW (PSP10016) — 0.048
  11. Huautla-2-redo-SW (PSP10030) — 0.050
  12. Maui-2-PS (PSP10041) — 0.050
  13. Z-strain-3-PS (PSP10084) — 0.050
  14. Maui-1-PS (PSP10040) — 0.052
  15. Maui-3-PS (PSP10042) — 0.053
  16. GoldenCoast-BAF-A1-UM (PSP10105) — 0.053
  17. GoldenCoast-BAF-A2-UM (PSP10106) — 0.054
  18. Orissa-India-ITW (PSP10071) — 0.054
  19. GoldenTeacher-3-SW (PSP10029) — 0.055
  20. Ecuador-3-SW (PSP10025) — 0.056

Most Distant

  1. Penvy-1-PS (PSP10045) — 0.718
  2. Penvy-Col5-PS (PSP10044) — 0.717
  3. Penvy-Col4-PS (PSP10043) — 0.717
  4. Penvy-2-SW (PSP10075) — 0.716
  5. Costa-Rica-1-redo-SW (PSP10022) — 0.665
  6. Costa-Rica-2-redo-SW (PSP10023) — 0.664
  7. Treasure-coast-1-PS (PSP10054) — 0.648
  8. Treasure-coast-2-PS (PSP10055) — 0.648
  9. Treasure-coast-3-PS (PSP10056) — 0.648
  10. Treasure-Coast-2-Mush (PSP10082) — 0.646
  11. Costa-Rica-3-redo-SW (PSP10024) — 0.635
  12. Bplus-ITW-WM (PSP10129) — 0.614
  13. Orissa-India-1-Mush (PSP10072) — 0.614
  14. Arenal-Volcano-1-Mush (PSP10059) — 0.612
  15. ColumbiaRust-1-SW (PSP10021) — 0.611
  16. Orissa-India-4-Mush (PSP10073) — 0.610
  17. Luminous-lucies-2-PS (PSP10032) — 0.609
  18. Luminous-lucies-3-PS (PSP10033) — 0.608
  19. Luminous-lucies-1-PS (PSP10034) — 0.608
  20. Roatan-Honduras-4-Mush (PSP10079) — 0.605

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 Puerto-Rican-ITW 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
096f9f1fbba3a129abf905eafa5b8ef8457e220bc429d7eac96afa645e8271ab
Stamping Certificate
Download PDF (39.8 KB)
SHASUM Hash
d054fa8631e4f1686d7d8d977493514f4ce47a204bbc948fb1ecae97edafb614

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