3 Results
3.1 GBS data assessment
The DNA extracted from the needles of the 148 individuals was genotyped
by GBS and returned a maximum of 4,822,890 and a minimum of 417,255
reads with an average of 1,630,465 raw reads per sample.
The raw reads were assembled into 14,565 filtered loci among the 148
individuals with an average of 11,285, a maximum of 14,003, and a
minimum of 2,209 loci per sample. A total of 91,203 SNPs with 28.6%
missing sites was detected by consensus base calling. An average of
0.02050 and 0.004297 estimated heterozygosity and error rate was
detected, respectively. Full statistical results are provided in
Appendix S4.
3.2 Spatial distribution of SNPs – Cluster analysis