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Table 6 Average allele read counts depending on which allele is in the reference genome

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

Allelea Reference genome Allele in reference genomea Overall True genotype
0 1 2
Reference Original Reference 1.483 2.470 1.237 0.017
Tailoredb Alternative 1.463 2.440 1.219 0.016
  Difference not aligned c 1.3% 1.2% 1.5% 9.8%
Alternative Original Reference 0.980 0.014 1.217 2.407
Tailoredb Alternative 0.993 0.016 1.234 2.438
  Difference not aligned c 1.3% 9.8% 1.3% 1.3%
  1. aAlleles are defined as reference or alternative allele based on the original pig reference genome Sscrofa11.1 (GenBank assembly accession: GCA_000003025.6)
  2. bThe tailored reference genome was created by replacing the reference allele with the alternative allele at all variant sites discovered across the 26 individuals with the 30× sequence data from chromosome 1
  3. cProportion of reads that did not align when the reference genome carried the opposite allele