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Table 1 Number of biallelic SNPs discovered on chromosome 1 with low and high sequencing coverage and percentage of overlap with the SNP genotyping array

From: Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

  Low coverage High coverage
Number of variants 1,333,943 1,693,308
Overlap with high-coverage data 96.9%
Overlap with low-coverage data 76.3%
Overlap with the SNP genotyping arraya 88.9% 95.7%
  1. aRelative to the 5779 variants present in the SNP genotyping array GGP-Porcine HD BeadChip (GeneSeek, Lincoln, NE) that segregated in the 26 individuals tested