This track depicts gaps in the assembly of the mouse genome.
Usage
data(mm10_gap)
Arguments
Value
data.frame that contain the gaps in the assembly of the mouse genome.
Format
A data frame with 686 observations on the following 4 variables.
Chrom
a character vector
Start
a numeric vector
End
a numeric vector
Name
a character vector
Details
This track depicts gaps in the assembly (Dec. 2011, Genome Reference Consortium
Mouse Build 38 (GCA_000001635.2)) of the mouse genome.
Gaps are represented as black boxes in this track. This assembly contains the
following principal types of gaps: (In this context, a contig is a set of
overlapping sequence reads.)
Clone - gaps between clones (114 gaps).
Contig - gaps between map contigs, various sizes (104 gaps).
Telomere - 42 gaps for telomeres (100,000 Ns)
Centromere - 20 gaps for centromeres (size: 2,890,000 Ns)
Short_arm - 21 gaps for the short arm (10,000 Ns) at base positions
100,001-110,000 of each chromosome.
other - sequence of Ns in the assembly that were not marked as gaps in the AGP
assembly definition file, various sizes (384 gaps).
Fragment - a single gap of 31 bases in chrX_GL456233_random.