Malabar-3-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.

psiT1 3 variants — 1 HIGH   2 MODERATE

psiT1

MODERATE E121G p.Glu121Gly missense A/G Both

chr10:1663786 98 of 98 reads

psiT1

MODERATE I214L p.Ile214Leu missense A/C Both

chr10:1664184 105 of 105 reads

psiT1

HIGH S223* p.Ser223Ter stop gained C/G Reads only

chr10:1664264 12 of 98 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 104 of 104 reads

between psiT1 and psiK

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

chr10:1666041 102 of 102 reads

psiK 1 variant — 1 MODERATE

psiK

MODERATE R173G p.Arg173Gly missense A/G Both

chr10:1666622 102 of 102 reads

psiH 3 variants — 3 MODERATE

psiH

MODERATE S7F p.Ser7Phe missense C/T Both

chr10:1667530 78 of 79 reads

psiH

MODERATE T502S p.Thr502Ser missense A/T Both

chr10:1669642 111 of 111 reads

psiH

MODERATE L508P p.Leu508Pro missense T/C Both

chr10:1669661 89 of 89 reads

psiM 1 variant — 1 MODERATE

psiM

MODERATE R102K p.Arg102Lys missense C/T Both

chr10:1674573 86 of 88 reads

psiD 2 variants — 2 MODERATE

psiD

MODERATE G206N p.Gly206Asn missense CC/TT Both

chr10:1676885 97 of 97 reads

psiD

MODERATE L22F p.Leu22Phe missense C/A Both

chr10:1677485 94 of 94 reads