Treasure-coast-2-PS

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.

psiR 1 variant — 1 MODERATE

psiR

MODERATE A344V p.Ala344Val missense G/A Both

chr10:1655743 45 of 47 reads

psiT1 6 variants — 6 MODERATE

psiT1

MODERATE E121G p.Glu121Gly missense A/G Both

chr10:1663786 51 of 51 reads

psiT1

MODERATE I214L p.Ile214Leu missense A/C Both

chr10:1664184 31 of 31 reads

psiT1

MODERATE T246I p.Thr246Ile missense C/T Both

chr10:1664333 36 of 36 reads

psiT1

MODERATE R266S p.Arg266Ser missense A/T Both

chr10:1664394 41 of 41 reads

psiT1

MODERATE L268I p.Leu268Ile missense C/A Both

chr10:1664398 40 of 40 reads

psiT1

MODERATE T386A p.Thr386Ala missense A/G Both

chr10:1664803 29 of 29 reads

between psiT1 and psiK 9 variants — 1 HIGH   8 MODERATE

between psiT1 and psiK

MODERATE A>G outside the coding sequence A/G Both

chr10:1665277 38 of 38 reads

between psiT1 and psiK

MODERATE A>G outside the coding sequence A/G Both

chr10:1665560 34 of 34 reads

between psiT1 and psiK

MODERATE G>A outside the coding sequence G/A Both

chr10:1665570 30 of 30 reads

between psiT1 and psiK

MODERATE A>C outside the coding sequence A/C Both

chr10:1665631 35 of 35 reads

between psiT1 and psiK

MODERATE G>A outside the coding sequence G/A Both

chr10:1665634 37 of 37 reads

between psiT1 and psiK

MODERATE A>G outside the coding sequence A/G Both

chr10:1665658 35 of 35 reads

between psiT1 and psiK

HIGH G>T outside the coding sequence G/T Both

chr10:1665665 39 of 39 reads

between psiT1 and psiK

MODERATE G>A outside the coding sequence G/A Both

chr10:1666040 41 of 41 reads

between psiT1 and psiK

MODERATE T>C outside the coding sequence T/C Both

chr10:1666041 41 of 41 reads

psiK 3 variants — 3 MODERATE

psiK

MODERATE S101A p.Ser101Ala missense T/G Both

chr10:1666406 48 of 48 reads

psiK

MODERATE V130A p.Val130Ala missense T/C Both

chr10:1666494 51 of 51 reads

psiK

MODERATE R173G p.Arg173Gly missense A/G Both

chr10:1666622 57 of 57 reads

psiH 1 variant — 1 MODERATE

psiH

MODERATE D214A p.Asp214Ala missense A/C Reads only

chr10:1668312 6 of 59 reads

psiT2 3 variants — 3 MODERATE

psiT2

MODERATE S139T p.Ser139Thr missense C/G Both

chr10:1671801 50 of 50 reads

psiT2

MODERATE G63D p.Gly63Asp missense C/T Both

chr10:1672192 45 of 45 reads

psiT2

MODERATE V31I p.Val31Ile missense C/T Both

chr10:1672289 68 of 68 reads

psiM 1 variant — 1 MODERATE

psiM

MODERATE R102K p.Arg102Lys missense C/T Both

chr10:1674573 47 of 47 reads

psiD 1 variant — 1 MODERATE

psiD

MODERATE L22F p.Leu22Phe missense C/A Both

chr10:1677485 75 of 75 reads