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NSF grant reports have documented the details, and specifics for the materials, preparation, characterization, and final assembly of the contig framework can be found in Coe E, Schaeffer ML (2005) Genetic, physical, maps, and database resources for maize. Ed Coe has made a copy of that paper available here What is a Reference Genome? What are the main changes between Ref Gen_v2 and Ref Gen_v3?

How can I map positions between the v2 and v3 assemblies?

The B73 seed source for B73-REF-REFERENCE-4.0 was also descended from PI 550473, but was maintained for several generations prior to being used as the source seed.Ed Coe reports that, "The results of QC lab checks for constancy in PI 550473 have been excellent." The same source was used for the IBM mapping population.Maps produced at Missouri used 302 lines of this population, providing unmatched precision (resolution is at the intra-BAC level).Improvements to order and orientation of within-BAC contigs using the minimum tiling path (MPT). Please report any assembly or gene model structure problems.

This includes misassembled regions, evidence for closing gaps, gene models that should be merged or split, evidence supporting low-confidence gene models, et cetera.Annotation was accomplished in the Ware laboratory at Cold Spring Harbor using the Maker pipeline (Campbell, 2014) and ~111,000 long read Pac Bio transcipts from six maize tissues.