Gaps in the B73 RefGen_v2 [from MGSC and AGI]This track highlights regions of the assembly where the sequence is not contiguous. There are three types of gaps. The number of Ns represents the TYPE of gap, NOT THE SIZE of the gap.
(1)Sequence "fragment" gaps: 100 or 200 Ns. The B73 reference genome was sequenced BAC by BAC. Each BAC sequence consists of pieces of contiguous sequence strung together. These gaps mark the position where the one contiguous sequence ends and another begins. The order and orientation between these sequence fragments often is not known. However, these sequence fragments do originate from a single BAC.
(2)"Contig" gaps: 1000 Ns between FPC contigs.
(3)"Clone" gaps: 500 Ns holding place for yet-to-be-sequenced clones.