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

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

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
  1. 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
  2. Values indicate the average across all replicates per sequencing method