Replicate comparison | Haplotyping level | GBS | MACE | WGS |
|---|
Pearson correlation | SNP level | 0.55 | 0.5 | 0.13 |
GH level | 0.64 | 0.59 | 0.91 |
MH level | 0.75 | 0.67 | 0.96 |
Contig level | 0.75 | 0.9 | 0.99 |
Negative Binomial | SNP level | < 0.001 | < 0.001 | < 0.001 |
GH level | < 0.001 | 0.007 | 0.67 |
MH level | 0.17 | 0.35 | 0.52 |
Contig level | 0.91 | 0.46 | 0.35 |
Zero inflated | SNP level | < 0.001 | 0.01 | < 0.001 |
GH level | < 0.001 | 0.01 | < 0.001 |
MH level | < 0.001 | 0.76 | 0.2 |
Contig level | 0.48 | 0.06 | 0.03 |
- Genotyping by sequencing (GBS), MACE transcriptome sequencing (MACE), and whole-genome re-sequencing (WGS). Haplotyping levels are: SNP—single nucleotide polymorphism (single data point); GH – gene-based haplotype (origin gene annotation model); MH—marker-based haplotype (origin from 9KiSelect genotyping chip); Contig—Contig haplotypes, in the text referred to as CH, windows of 100 kb size. Pearson correlation—correlation of the pool genotyping replicates (P1-P3) to each other, for each haplotyping level and genotyping approach. Negative binomial/zero inflated—probability values from a generalized linear model, based on a negative binomial and zero inflated distribution. Both distributions are necessary to cover the entirety of the allele frequency distribution per locus
