Skip to main content

Table 2 Frequency of discordant SNP calls across 16 individuals genotyped twice on each array

From: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

Array

SNP subset Groups and their percentage (%) discordant*SNP calls

1

2

3

4

5

6

Infinium

0.0016

0.0014

Axiom

0.3199

0.0706

0.0134

0.0117

0.1516

0.0421

  1. *For accessions that were genotyped more than twice on an array, a single average value was used in the across accession analyses
  2. Subset 1: 10,295 SNPs from the Infinium array that passed the SNP data curation steps in the present study.
  3. Subset 2: 8412 SNPs considered compatible between the array platforms in this study.
  4. Subset 3: 275,223 SNPs in the Axiom array deemed robust [34].
  5. Subset 4: 253,095 SNPs from subset 3 filtered for absence of more than one Mendelian inconsistent error in Muranty et al. [32].
  6. Subset 5: 402,714 SNPs in the Axiom array that were classified as “Poly High Resolution” or “No Minor Homozygous” by Axiom Analysis Suite software.
  7. Subset 6: 320,761 SNPs from subset 5 with SNPs removed that had Mendelian inconsistent errors in two or more parent-offspring relationships, discordant SNP calls in two or more duplicate pairs, or were heterozygous in doubled haploid accessions from Muranty et al. [32]