Advanced Strain Search

Orissa-India-1-Mush

PSP 10072

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 83 of 110 cultivars (76th percentile).

Clonal or not?

Assessing…

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

Clone Test

Is Orissa-India-1-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-1-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 2 variants — 2 MODERATE
psiT1
MODERATE K166Q p.Lys166Gln missense A/C Reads only
chr10:1663979 3 of 31 reads
psiT1
MODERATE A292S p.Ala292Ser missense G/T Reads only
chr10:1664470 4 of 27 reads
between psiT1 and psiK 1 variant — 1 MODERATE
between psiT1 and psiK
MODERATE C>A outside the coding sequence C/A Reads only
chr10:1665646 4 of 20 reads
psiK 1 variant — 1 MODERATE
psiK
MODERATE E167G p.Glu167Gly missense A/G Reads only
chr10:1666605 3 of 18 reads
psiH 8 variants — 8 MODERATE
psiH
MODERATE D121E p.Asp121Glu missense C/A Reads only
chr10:1667977 25 of 74 reads
psiH
MODERATE R127G p.Arg127Gly missense A/G Reads only
chr10:1667993 7 of 78 reads
psiH
MODERATE S135T p.Ser135Thr missense G/C Reads only
chr10:1668018 12 of 72 reads
psiH
MODERATE G138N p.Gly138Asn missense GG/AA Reads only
chr10:1668026 10 of 33 reads
psiH
MODERATE K140R p.Lys140Arg missense A/G Reads only
chr10:1668033 10 of 30 reads
psiH
MODERATE H151N p.His151Asn missense C/A Reads only
chr10:1668065 13 of 36 reads
psiH
MODERATE D404N p.Asp404Asn missense G/A Reads only
chr10:1669172 15 of 41 reads
psiH
MODERATE V407E p.Val407Glu missense T/A Reads only
chr10:1669182 15 of 43 reads
psiM 1 variant — 1 HIGH
psiM
HIGH C119* p.Cys119Ter stop gained A/T Reads only
chr10:1674466 2 of 17 reads
psiD 5 variants — 5 MODERATE
psiD
MODERATE I310V p.Ile310Val missense T/C Reads only
chr10:1676574 10 of 35 reads
psiD
MODERATE V307L p.Val307Leu missense C/G Reads only
chr10:1676583 10 of 35 reads
psiD
MODERATE L286I p.Leu286Ile missense G/T Reads only
chr10:1676646 11 of 32 reads
psiD
MODERATE N208T p.Asn208Thr missense T/G Reads only
chr10:1676879 19 of 45 reads
psiD
MODERATE Q93H p.Gln93His missense C/G Reads only
chr10:1677223 12 of 43 reads

Genetic Relatives

Nearest

  1. Orissa-India-4-Mush (PSP10073) — 0.094
  2. Penvy-1-PS (PSP10045) — 0.173
  3. Penvy-2-SW (PSP10075) — 0.173
  4. Penvy-Col5-PS (PSP10044) — 0.173
  5. Penvy-Col4-PS (PSP10043) — 0.173
  6. MGC_2016_unknown_strain (PSP10012) — 0.331
  7. Z-strain-1-Mush (PSP10083) — 0.333
  8. Costa-Rica-1-redo-SW (PSP10022) — 0.338
  9. Costa-Rica-2-redo-SW (PSP10023) — 0.341
  10. Costa-Rica-3-redo-SW (PSP10024) — 0.348
  11. Bplus-ITW-WM (PSP10129) — 0.349
  12. Roatan-Honduras-4-Mush (PSP10079) — 0.354
  13. ColumbiaRust-1-SW (PSP10021) — 0.355
  14. Treasure-Coast-2-Mush (PSP10082) — 0.358
  15. Treasure-coast-3-PS (PSP10056) — 0.360
  16. Treasure-coast-1-PS (PSP10054) — 0.360
  17. Treasure-coast-2-PS (PSP10055) — 0.361
  18. Arenal-Volcano-1-Mush (PSP10059) — 0.361
  19. Tosohatchee-print-ITW (PSP10081) — 0.364
  20. Luminous-lucies-2-PS (PSP10032) — 0.366

Most Distant

  1. Bplus-3-PS (PSP10001) — 0.617
  2. Huautla-3-redo-SW (PSP10031) — 0.616
  3. Huautla-2-redo-SW (PSP10030) — 0.616
  4. Huautla-3-PS (PSP10005) — 0.616
  5. GoldenCoast-BAF-B1-UM (PSP10107) — 0.614
  6. Puerto-Rican-ITW (PSP10078) — 0.614
  7. GoldenCoast-BAF-B2-UM (PSP10108) — 0.614
  8. Maui-2-PS (PSP10041) — 0.613
  9. Bplus-2-redo-SW (PSP10015) — 0.612
  10. GoldenCoast-BAF-A1-UM (PSP10105) — 0.612
  11. Maui-1-PS (PSP10040) — 0.612
  12. Bplus-1-redo-SW (PSP10014) — 0.611
  13. Bplus-3-redo-SW (PSP10016) — 0.611
  14. Maui-3-PS (PSP10042) — 0.611
  15. GoldenCoast-BAF-A2-UM (PSP10106) — 0.611
  16. GoldenTeacher-3-SW (PSP10029) — 0.610
  17. Orissa-India-ITW (PSP10071) — 0.610
  18. Ecuador-3-SW (PSP10025) — 0.610
  19. Gulf-Coast-BAF (PSP10090) — 0.610
  20. Gulf-Coast (PSP10091) — 0.610

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-1-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
387bbc683294cb9aaf7cd1ef23a53bff6d38077d547c9339102e26d05553548d
Stamping Certificate
Download PDF (39.5 KB)
SHASUM Hash
315a6829d505f3299eafe04ae4b86e76c85f7b20540cd6fb1847100365f37873

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