Q:
I believe I have discovered numerous errors in the NA12878 dataset. We are working with the most recent version,
NA12878_diploid_genome_may3_2011. They are all single base pair mismatches between the paternal and maternal chromosomes in regions that the accompanying .map file marks as contigs.

A:
.map file shows continuous equivalent (without gaps) blocks between haplotypes. BUT THEY DO INCLUDE SNPs. So, heterozygous SNPs will result in base mismatch within a block.