Advanced Strain Search

Orissa-India-4-Mush

PSP 10073

DNA Source: Mushrooms.com

General Information

Accession Date
June 13, 2021
Report Type
Whole-Genome Sequencing
DNA Source Website
mushrooms.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: Uncommon

More genetically distinct than 73 of 110 cultivars (67th percentile).

Clonal or not?

Assessing…

Interactive 3D Psilocybe Atlas See Orissa-India-4-Mush in the tree of life Spin, zoom, and explore exactly where Orissa-India-4-Mush sits among its closest genetic relatives. Launch 3D tree

Clone Test

Is Orissa-India-4-Mush 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 Orissa-India-4-Mush 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 6 variants — 1 HIGH   5 MODERATE
psiT1
MODERATE E121G p.Glu121Gly missense A/G Reads only
chr10:1663786 25 of 66 reads
psiT1
HIGH G>A splice acceptor G/A Reads only
chr10:1663847 9 of 54 reads
psiT1
MODERATE I214L p.Ile214Leu missense A/C Reads only
chr10:1664184 13 of 55 reads
psiT1
MODERATE T246I p.Thr246Ile missense C/T Reads only
chr10:1664333 5 of 50 reads
psiT1
MODERATE R266S p.Arg266Ser missense A/T Reads only
chr10:1664394 7 of 51 reads
psiT1
MODERATE T386A p.Thr386Ala missense A/G Reads only
chr10:1664803 11 of 59 reads
between psiT1 and psiK 9 variants — 1 HIGH   8 MODERATE
between psiT1 and psiK
MODERATE A>G outside the coding sequence A/G Reads only
chr10:1665277 19 of 72 reads
between psiT1 and psiK
MODERATE A>G outside the coding sequence A/G Reads only
chr10:1665560 10 of 52 reads
between psiT1 and psiK
MODERATE G>A outside the coding sequence G/A Reads only
chr10:1665570 7 of 50 reads
between psiT1 and psiK
MODERATE A>C outside the coding sequence A/C Reads only
chr10:1665631 6 of 50 reads
between psiT1 and psiK
MODERATE G>A outside the coding sequence G/A Reads only
chr10:1665634 6 of 51 reads
between psiT1 and psiK
MODERATE A>G outside the coding sequence A/G Reads only
chr10:1665658 8 of 55 reads
between psiT1 and psiK
HIGH G>T outside the coding sequence G/T Reads only
chr10:1665665 10 of 59 reads
between psiT1 and psiK
MODERATE G>A outside the coding sequence G/A Reads only
chr10:1666040 10 of 57 reads
between psiT1 and psiK
MODERATE T>C outside the coding sequence T/C Reads only
chr10:1666041 11 of 57 reads
psiK 6 variants — 6 MODERATE
psiK
MODERATE K43E p.Lys43Glu missense A/G Reads only
chr10:1666169 8 of 60 reads
psiK
MODERATE S101A p.Ser101Ala missense T/G Both
chr10:1666406 20 of 71 reads
psiK
MODERATE L110V p.Leu110Val missense T/G Both
chr10:1666433 23 of 69 reads
psiK
MODERATE E167G p.Glu167Gly missense A/G Reads only
chr10:1666605 6 of 47 reads
psiK
MODERATE R173G p.Arg173Gly missense A/G Reads only
chr10:1666622 19 of 45 reads
psiK
MODERATE Q279L p.Gln279Leu missense A/T Reads only
chr10:1666941 14 of 44 reads

Genetic Relatives

Nearest

  1. Orissa-India-1-Mush (PSP10072) — 0.094
  2. Penvy-2-SW (PSP10075) — 0.192
  3. Penvy-1-PS (PSP10045) — 0.192
  4. Penvy-Col5-PS (PSP10044) — 0.192
  5. Penvy-Col4-PS (PSP10043) — 0.192
  6. Roatan-Honduras-4-Mush (PSP10079) — 0.300
  7. MGC_2016_unknown_strain (PSP10012) — 0.301
  8. Z-strain-1-Mush (PSP10083) — 0.316
  9. Costa-Rica-3-redo-SW (PSP10024) — 0.331
  10. Costa-Rica-1-redo-SW (PSP10022) — 0.331
  11. Costa-Rica-2-redo-SW (PSP10023) — 0.333
  12. Arenal-Volcano-1-Mush (PSP10059) — 0.337
  13. Bplus-ITW-WM (PSP10129) — 0.338
  14. Luminous-lucies-2-PS (PSP10032) — 0.340
  15. Luminous-lucies-1-PS (PSP10034) — 0.340
  16. Luminous-lucies-3-PS (PSP10033) — 0.340
  17. Treasure-Coast-2-Mush (PSP10082) — 0.340
  18. Treasure-coast-3-PS (PSP10056) — 0.342
  19. Treasure-coast-1-PS (PSP10054) — 0.343
  20. Treasure-coast-2-PS (PSP10055) — 0.343

Most Distant

  1. Bplus-3-PS (PSP10001) — 0.617
  2. GoldenCoast-BAF-B1-UM (PSP10107) — 0.613
  3. GoldenCoast-BAF-B2-UM (PSP10108) — 0.613
  4. GoldenCoast-BAF-A1-UM (PSP10105) — 0.613
  5. GoldenCoast-BAF-A2-UM (PSP10106) — 0.611
  6. Puerto-Rican-ITW (PSP10078) — 0.610
  7. Orissa-India-ITW (PSP10071) — 0.610
  8. Huautla-2-redo-SW (PSP10030) — 0.610
  9. Huautla-3-redo-SW (PSP10031) — 0.609
  10. Huautla-3-PS (PSP10005) — 0.609
  11. Gulf-Coast-BAF (PSP10090) — 0.608
  12. Gulf-Coast (PSP10091) — 0.608
  13. True-Albino-Teacher-ITW-WM (PSP10140) — 0.608
  14. Bplus-2-redo-SW (PSP10015) — 0.607
  15. Bplus-1-redo-SW (PSP10014) — 0.606
  16. Bplus-3-redo-SW (PSP10016) — 0.606
  17. Ecuador-3-SW (PSP10025) — 0.606
  18. Maui-2-PS (PSP10041) — 0.606
  19. GoldenTeacher-3-SW (PSP10029) — 0.606
  20. Avery-Albino-ITW-WM (PSP10123) — 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 Orissa-India-4-Mush 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
93f67d9c357b99fba5cad00ae91ae4bc50522bca5cd4300d162ca0e52cba432a
Stamping Certificate
Download PDF (39.4 KB)
SHASUM Hash
c044ed2ffa2d9efb8a049f67e17b6c8dc5e3b283bedd5f20f85bb407b50239b4

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