Screenshot of the SeqMan (DNASTAR) visualization of contig456 showing 2 alleles at a single locus. Boxes 1 and 2 represent unique haplotypes obtained from the NGen 3.0 assembly of the 454 reads from Bing and Rainier according to the filtering parameters described in the methods. These haplotypes differ at each of the bases labeled in green on one of the haplotypes for a total of 10 SNPs between these haplotypes. Haplotype 1 consists of 11 reads from Bing and 1 of Rainier while haplotype 2 is entirely Rainier.
Koepke et al. BMC Genomics 2012 13:18 doi:10.1186/1471-2164-13-18