mm10_gap {chromPlot} | R Documentation

## Gaps

### Description

This track depicts gaps in the assembly of the mouse genome.

### Usage

    data(mm10_gap)

### 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.

### Value

data.frame that contain the gaps in the assembly of the mouse genome.

### Examples

    data(mm10_gap)
    ## maybe str(mm10_gap) ; plot(mm10_gap) ...

[Package chromPlot version 1.8.0 Index]