Advanced Strain Search

Malabar-1-PS

PSP 10037

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 38 of 110 cultivars (35th percentile).

Clonal or not?

Assessing…

Interactive 3D Psilocybe Atlas See Malabar-1-PS in the tree of life Spin, zoom, and explore exactly where Malabar-1-PS sits among its closest genetic relatives. Launch 3D tree

Clone Test

Is Malabar-1-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 Malabar-1-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.

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 69 of 69 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 73 of 74 reads
between psiT1 and psiK
MODERATE T>C outside the coding sequence T/C Both
chr10:1666041 76 of 76 reads
psiK 1 variant — 1 MODERATE
psiK
MODERATE R173G p.Arg173Gly missense A/G Both
chr10:1666622 79 of 79 reads
psiH 3 variants — 3 MODERATE
psiH
MODERATE S7F p.Ser7Phe missense C/T Both
chr10:1667530 57 of 57 reads
psiH
MODERATE T502S p.Thr502Ser missense A/T Both
chr10:1669642 64 of 64 reads
psiH
MODERATE L508P p.Leu508Pro missense T/C Both
chr10:1669661 61 of 61 reads
psiM 1 variant — 1 MODERATE
psiM
MODERATE R102K p.Arg102Lys missense C/T Both
chr10:1674573 81 of 81 reads
psiD 2 variants — 2 MODERATE
psiD
MODERATE G206N p.Gly206Asn missense CC/TT Both
chr10:1676885 55 of 55 reads
psiD
MODERATE L22F p.Leu22Phe missense C/A Both
chr10:1677485 79 of 79 reads

Genetic Relatives

Nearest

  1. Malabar-3-PS (PSP10039) — 0.015
  2. Malabar-2-PS (PSP10038) — 0.015
  3. Malabar-2-SW (PSP10035) — 0.015
  4. Malabar-3-SW (PSP10036) — 0.016
  5. Mazatapec-2-SW (PSP10006) — 0.049
  6. Mazatapec-cube-1-Mush (PSP10068) — 0.063
  7. WFB-UM-WM (PSP10121) — 0.274
  8. WFB-UM (PSP10112) — 0.274
  9. BM1b-UM-WM (PSP10125) — 0.322
  10. Mazatapec (PSP10093) — 0.324
  11. BM1-UM (PSP10098) — 0.347
  12. BM16 (PSP10087) — 0.358
  13. Samui-2-PS (PSP10048) — 0.381
  14. Orissa-India-print-ITW (PSP10074) — 0.392
  15. GoldenTeacher-1-SW (PSP10027) — 0.404
  16. PES-2-SW (PSP10008) — 0.406
  17. KOH-Samui-1-ITW (PSP10063) — 0.408
  18. Thailand-Koh-Samui-1-Mush (PSP10080) — 0.408
  19. Maui-2-PS (PSP10041) — 0.409
  20. Ecuador-3-PS (PSP10061) — 0.409

Most Distant

  1. Albino-Aplus-1-SW (PSP10013) — 0.508
  2. Penvy-Col5-PS (PSP10044) — 0.503
  3. Penvy-1-PS (PSP10045) — 0.503
  4. Penvy-Col4-PS (PSP10043) — 0.502
  5. Penvy-2-SW (PSP10075) — 0.502
  6. Aplusplus (PSP10085) — 0.502
  7. Panaeolus-Copelandia-Tropicalis-2-Mush (PSP10077) — 0.495
  8. Costa-Rica-1-redo-SW (PSP10022) — 0.494
  9. Costa-Rica-2-redo-SW (PSP10023) — 0.487
  10. AAplus-4-Mush (PSP10057) — 0.487
  11. Leucistic_GT2-ITW (PSP10067) — 0.486
  12. Albino-Aplus-3-PS (PSP10000) — 0.486
  13. Orissa-India-1-Mush (PSP10072) — 0.486
  14. Escondido-Mexico-1-Mush (PSP10062) — 0.477
  15. Leucistic_GT1-ITW (PSP10066) — 0.473
  16. Costa-Rica-3-redo-SW (PSP10024) — 0.466
  17. Amazon-ITW-WM (PSP10122) — 0.465
  18. Costa-Rica-1-redo-SW (PSP10003) — 0.464
  19. APlusPlus-Leucistic-ITW (PSP10058) — 0.463
  20. Orissa-India-4-Mush (PSP10073) — 0.462

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 Malabar-1-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
07c456a5bb6a7b4ff7c4a2a1104afdfbf99aa0e417b525e46b879a4d5076c2d8
Stamping Certificate
Download PDF (39.4 KB)
SHASUM Hash
6fbf9e71320134b628c026628c5262bb3171bfcb4bcd2320d341c7206cb8475f

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