#Major allele reference sequences from 
#Dewey, et al. PLoS Genet 7(9):e1002280.
#These reference sequences are built using coordinates from the Feb. 2009 assembly of the human genome (hg19, GRCh 37.1, GCA_000001405.1)
#Repeats are soft-masked (shown in lower case)
#1000 genomes project pilot phase data for CEU, CHB/JPT, and YRI was used to derive the major allele at every position cataloged
#This major allele was substituted for the reference base at every position at which the NCBI reference contained the minor allele
#Repeat masking was preserved across these substituted bases
#Base changes (number of positions changed):
#	CEU: 1,543,755
#	YRI: 1,658,360
#	CHB/JPT: 1,676,213
#These files are in zipped, karyotypically-sorted combined fasta files, including chrX, chrY, and chrM (from the revised Cambridge Reference Sequence for human mitochondrial DNA NC_012920)
#For publications using these sequences, please cite: Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, et al. (2011). Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence. PLoS Genet 7(9): e1002280. doi:10.1371/journal.pgen.1002280