Description

Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap.

This assembly contains the following principal types of gaps:

• clone - gaps on chromosomes to represent telomere sequence at the beginning of chromosomes
• fragment - gaps between the Whole Genome Shotgun contigs of a scaffold or ultracontig. These are represented by varying numbers of Ns in the assembly. In this context, a contig is a set of overlapping sequence reads and a scaffold is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads. Contig gap sizes are usually taken from read pair data.

See also: UTGB Medaka Genome at the Morishita Laboratory.