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

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

	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

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

ISSN: 1746-4811