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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