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

Table 1 Descriptive statistics for the three sequencing methods genotyping by sequencing (GBS), MACE transcriptome sequencing (MACE), and whole-genome re-sequencing (WGS)

Stats	Haplotyping level	GBS	MACE	WGS
Number of identified haplotypes	SNP	82,435	13,079	3,991,259
	GH	17,026	5919	34,344
	MH	4702	3275	5946
	Contig	483	460	485
Median read count per haplotype	SNP	6	11	9
	GH	39	21	494
	MH	234	36	2440
	Contig	2645	238	74,134
Average read count per haplotype	SNP	28	25	9.1
	GH	137	42	963
	MH	450	70	5443
	Contig	4837	520	74,855
Variance read count over haplotypes	SNP	3329	348	14.91
	GH	62,413	4,109	2 × 10⁶
	MH	4,30,575	9,482	1.46 × 10⁸
	Contig	2,9*10⁷	4,69,851	1.03 × 10⁹
Genome wide allele frequency	SNP	7.48%	7.06%	6.54%
	GH	7.48%	7.09%	6.56%
	MH	7.43%	7.02%	6.56%
	Contig	7.48%	7.06%	6.54%
Median SNP count per haplotype	GH	3	1	55
	MH	8	2	272
	Contig	142	2	8250
Mean SNP count per haplotype	GH	4	2	106
	MH	14	4	598
	Contig	154	26	8216

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
Values indicate the average across all replicates per sequencing method

ISSN: 1746-4811