Allele coverage not reaching 100%

[Ira Herniter]

I'm trying to determine how many individuals I need to reach 95% allele coverage, so I've been using the "Coverage" option in the CoreHunter GUI.

My dataset consists of 76 individuals, and I've tested a range of core sizes, but for some reason the allele coverage seems to max out at 75%, even when I include all but one of my genotypes. I've repeatedly run the analysis with a designated core size of 75/76, and I keep getting the same score. My results are as follows:

#taxa CV
10 0.7058
15 0.7209
20 0.7292
25 0.7352
30 0.7398
35 0.7431
40 0.7458
45 0.7480
50 0.7497
55 0.7512
60 0.7524
65 0.7532
70 0.7537
75 0.7541

Thanks,

Ira

[Herman De Beukelaer]

Hi Irna,

Thanks for reaching out. Would it be possible to share your data, anonymized if needed? What data format are you using? My first guess would be that there are some loci in your dataset for which some alleles are not present in any of your accessions, which would mean you cannot get 100% allele coverage for these loci regardless of what selection you make.

Kind regards

Herman

Op maandag 1 september 2025 om 16:52:03 UTC+2 schreef iher...@gmail.com: