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Table 1 Sequence error estimation

From: Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses

Number of SNPs Horse 4 Horse 5 Horse 6 Horse 7 Horse 9
Hanoverian Hanoverian Hanoverian Hanoverian Arabian
Heterozygous in NGS data 891,514 815,810 833,149 832,549 812,952
Heterozygous in BeadChip data 16,426 15,469 15,873 15,987 14,008
Homozygous in BeadChip data 33,403 34,360 33,956 33,842 35,821
Heterozygous in NGS and BeadChip data 3,555 (7.14 %) 3,239 (6.50 %) 3,306 (6.64 %) 3,396 (6.82 %) 2,960 (5.94 %)
Heterozygous in BeadChip and homozygous in NGS data 12,867 (25.83 %) 12,223 (24.54 %) 12,565 (25.22 %) 12,589 (25.27 %) 11,047 (22.17 %)
(False-negative rate)
Homozygous in BeadChip and heterozygous in NGS data 19 (3.8 × 10−4of all 49,813 positions validated in BeadChip) 29 (5.8 × 10−4of all 49,813 positions validated in BeadChip) 38 (7.6 × 10−4of all 49,815 positions validated in BeadChip) 49 (9.8 × 10−4of all 49,823 positions validated in BeadChip) 28 (5.6 × 10−4of all 49,824 positions validated in BeadChip)
(False-positive rate)
Homozygous in >10 Mb BeadChip ROH regions and heterozygous in NGS data 5.9 × 10−5 3.8 × 10−5 2.2 × 10−5 3.1 × 10−4 2.6 × 10−5
(Robust false-positive rate)
  1. Number of detected Next Generation sequencing (NGS) -SNPs and their sequence error rates in comparison to Illumina SNP50 BeadChip data. The BeadChip data are assumed to be error free