03 / Notes
Notes
The pieces of knowledge you need along the way, written up one at a time. There is no need to read them in order — start wherever you are stuck.
- 2026.08.12 Annotate
Which table decided that phenotype?
The genotype is in your data. The phenotype is not — it comes from an external published table that maps one to the other. So write down which table, and which version, you consulted.
- 2026.08.12 Verify
Sorting "nothing came up" into three
The rsID you were looking for is absent from your results. Was it the same as the reference, was the position never read, or is it a kind this method cannot read at all? All three look like "no match" and none of them mean the same thing.
- 2026.08.12 Annotate
In your population, that variant may be ordinary
Rarity flips depending on which population you measure it against. Decide in advance where your frequencies come from, and "rare, therefore a weakness" stops being a reading you can make by accident.
- 2026.08.06 Groundwork
What whole-genome sequencing can and cannot read
Whole-genome does not mean everything is legible. Before starting the reading, it pays to know which regions are unreadable in principle.
- 2026.08.05 Verify
Different reference builds put the coordinates in different places
The same variant, but the position differs between your data and the source you are reading. Usually the reference genome builds do not match. Check this first.
- 2026.08.04 Normalise
When a genotype looks reversed — strand mix-ups
The literature talks about C and T; your data only shows G and A. Nothing has been misread. The two are written against different strands.