Skip to main content

Table 2 Individual genotyping of selected KASP markers compared to pool sequencing (P1)

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

  Haplotyping level GBS MACE WGS
RMSE SNP level 0.07 0.15
GH level 0.11 0.04 0.03
MH level 0.06 0.04 0.03
Contig level 0.03 0.04 0.03
Stat test negative binomial level SNP level 0.67 0.02
GH level 0.35 0.99 0.57
MH level 0.47 0.94 0.39
Contig level 0.59 0.28 0.46
Stat test zero inflated level SNP level 0.68 0.09
GH level 0.15 0.64 0.64
MH level 0.62 0.67 0.63
Contig level 0.44 0.62 0.53
Pearson Residual width SNP level 3.85% 3.37%
GH level 3.78% 3.70% 3.49%
MH level 3.77% 3.89% 3.40%
Contig level 3.60% 3.92% 3.95%
Pearson correlation SNP level 0.79 0.93
GH level 0 0.9 0.97
MH level 0.83 0.93 0.96
Contig level 0.94 0.88 0.95
Median read coverage of haplotypes in pool sample per KASP marker SNP level 41 51 7
GH level 51 82 607
MH level 575 158 7749
Contig level 10,122 917 81,186
Count of matched KASP markers to pool seq SNP level 1 19 11
GH level 15 16 15
MH level 17 17 17
Contig level 19 19 19
  1. Genotyping by sequencing (GBS), MACE transcriptome sequencing (MACE), and whole-genome re-sequencing (WGS) (P1 sample). 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. RMSE = root mean square error of pool to individual genotyping on different haplotyping levels for three different genotyping approaches. Stat test rows present the probability value, where p < 0.05 indicates significant variations between individual and pool genotyping. Pearson residual width—average deviation of pool haplotype allele frequency estimate to individual genotyping. Pearson correlation—correlation of pool to individual genotyping, for each haplotyping level and genotyping approach