Costa-Rica-3-redo-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.

psiT1 7 variants — 2 HIGH   5 MODERATE

psiT1

MODERATE E121G p.Glu121Gly missense A/G Reads only

chr10:1663786 10 of 10 reads

psiT1

MODERATE I214L p.Ile214Leu missense A/C Reads only

chr10:1664184 9 of 9 reads

psiT1

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

chr10:1664264 3 of 6 reads

psiT1

MODERATE T246I p.Thr246Ile missense C/T Reads only

chr10:1664333 4 of 4 reads

psiT1

MODERATE R266S p.Arg266Ser missense A/T Reads only

chr10:1664394 6 of 6 reads

psiT1

MODERATE T386A p.Thr386Ala missense A/G Reads only

chr10:1664803 11 of 11 reads

psiT1

HIGH L461* p.Leu461Ter stop gained T/A Reads only

chr10:1665085 2 of 15 reads

between psiT1 and psiK 9 variants — 1 HIGH   8 MODERATE

between psiT1 and psiK

MODERATE A>G outside the coding sequence A/G Reads only

chr10:1665277 8 of 8 reads

between psiT1 and psiK

MODERATE A>G outside the coding sequence A/G Reads only

chr10:1665560 9 of 9 reads

between psiT1 and psiK

MODERATE G>A outside the coding sequence G/A Reads only

chr10:1665570 10 of 10 reads

between psiT1 and psiK

MODERATE A>C outside the coding sequence A/C Reads only

chr10:1665631 8 of 8 reads

between psiT1 and psiK

MODERATE G>A outside the coding sequence G/A Reads only

chr10:1665634 8 of 8 reads

between psiT1 and psiK

MODERATE A>G outside the coding sequence A/G Reads only

chr10:1665658 7 of 7 reads

between psiT1 and psiK

HIGH G>T outside the coding sequence G/T Reads only

chr10:1665665 10 of 10 reads

between psiT1 and psiK

MODERATE G>A outside the coding sequence G/A Reads only

chr10:1666040 8 of 8 reads

between psiT1 and psiK

MODERATE T>C outside the coding sequence T/C Reads only

chr10:1666041 9 of 9 reads

psiK 5 variants — 5 MODERATE

psiK

MODERATE S101A p.Ser101Ala missense T/G Reads only

chr10:1666406 12 of 12 reads

psiK

MODERATE L110V p.Leu110Val missense T/G Reads only

chr10:1666433 8 of 8 reads

psiK

MODERATE E167G p.Glu167Gly missense A/G Reads only

chr10:1666605 18 of 18 reads

psiK

MODERATE R173G p.Arg173Gly missense A/G Reads only

chr10:1666622 20 of 20 reads

psiK

MODERATE Q279L p.Gln279Leu missense A/T Reads only

chr10:1666941 6 of 6 reads

psiH 1 variant — 1 MODERATE

psiH

MODERATE K236N p.Lys236Asn missense G/T Reads only

chr10:1668429 4 of 4 reads

psiT2 3 variants — 3 MODERATE

psiT2

MODERATE E291Q p.Glu291Gln missense C/G Assembly only

chr10:1671235 6 of 6 reads

psiT2

MODERATE S139T p.Ser139Thr missense C/G Both

chr10:1671801 11 of 11 reads

psiT2

MODERATE G63D p.Gly63Asp missense C/T Both

chr10:1672192 9 of 9 reads

psiM 2 variants — 1 HIGH   1 MODERATE

psiM

MODERATE R102K p.Arg102Lys missense C/T Reads only

chr10:1674573 14 of 14 reads

psiM

HIGH T>A splice acceptor T/A Reads only

chr10:1674655 4 of 10 reads

psiD 1 variant — 1 MODERATE

psiD

MODERATE L22F p.Leu22Phe missense C/A Reads only

chr10:1677485 7 of 7 reads

Fvcpc2 1 variant — 1 MODERATE

Fvcpc2

MODERATE p.Ser201Pro c.601T>C missense variant T/C

CM038999.1:1973492