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Table 1 Allele-aware alignments with complete genotypes (GSNAP) vs no genotype information (BWA)

From: Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

  GSNAP BWA
  Standard Complementa Differenceb Standard Complementa Differenceb
Reads mapped uniquely 33,599,679 33,599,721 120 33,543,808 33,547,947 344,942
Reads at heterozygous sites 1,295,901 1,295,914 120 1,197,696 1,186,891 344,942
  Reference allele 675,394 620,517 - 677,697 640,978 -
  Non-reference allele 620,507 675,397 - 519,999 545,913 -
Peaks at heterozygous sites c 1618 1618 0 1593 1614 87
Allelic imbalance sites identified d 200 200 0 151 147 56
  Reference allele 108 92 - 91 82 -
  Non-reference allele 92 108 - 60 65 -
  1. aAlignment reference contained the non-reference allele of heterozygous sites used to create the standard reference bDiffers in mapping or detection between alignments to standard and complement references cOut of 10,000 peaks with strongest signal dbinomial p-value < .01