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Table 3 Comparison of the replicates for each sequencing method

From: High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing

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
  1. 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