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

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

	GSNAP			BWA
	Standard	Complement^a	Difference^b	Standard	Complement^a	Difference^b
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	-

^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

ISSN: 1755-8794