Chitwan-1-SW

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 92 of 185 reads

psiT1 6 variants — 6 MODERATE

psiT1

MODERATE E121G p.Glu121Gly missense A/G Both

chr10:1663786 184 of 184 reads

psiT1

MODERATE I214L p.Ile214Leu missense A/C Both

chr10:1664184 176 of 176 reads

psiT1

MODERATE T246I p.Thr246Ile missense C/T Both

chr10:1664333 128 of 132 reads

psiT1

MODERATE R266S p.Arg266Ser missense A/T Both

chr10:1664394 111 of 115 reads

psiT1

MODERATE L268I p.Leu268Ile missense C/A Both

chr10:1664398 54 of 115 reads

psiT1

MODERATE T386A p.Thr386Ala missense A/G Both

chr10:1664803 151 of 151 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 115 of 115 reads

between psiT1 and psiK

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

chr10:1665560 168 of 171 reads

between psiT1 and psiK

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

chr10:1665570 165 of 168 reads

between psiT1 and psiK

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

chr10:1665631 147 of 150 reads

between psiT1 and psiK

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

chr10:1665634 146 of 149 reads

between psiT1 and psiK

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

chr10:1665658 174 of 176 reads

between psiT1 and psiK

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

chr10:1665665 177 of 179 reads

between psiT1 and psiK

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

chr10:1666040 128 of 128 reads

between psiT1 and psiK

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

chr10:1666041 136 of 136 reads

psiK 6 variants — 6 MODERATE

psiK

MODERATE R90W p.Arg90Trp missense C/T Both

chr10:1666373 108 of 184 reads

psiK

MODERATE S101A p.Ser101Ala missense T/G Both

chr10:1666406 209 of 209 reads

psiK

MODERATE L110V p.Leu110Val missense T/G Both

chr10:1666433 200 of 204 reads

psiK

MODERATE E167G p.Glu167Gly missense A/G Reads only

chr10:1666605 64 of 155 reads

psiK

MODERATE R173G p.Arg173Gly missense A/G Both

chr10:1666622 158 of 158 reads

psiK

MODERATE Q279L p.Gln279Leu missense A/T Both

chr10:1666941 184 of 186 reads

psiM 1 variant — 1 MODERATE

psiM

MODERATE R102K p.Arg102Lys missense C/T Both

chr10:1674573 91 of 154 reads

psiD 1 variant — 1 MODERATE

psiD

MODERATE L22F p.Leu22Phe missense C/A Reads only

chr10:1677485 81 of 184 reads