build36: NCBI build 36 data for Affymetrix 5K Mouse Kit

In byandell/qtlview: Visualization of QTL Scans for Multiple Traits

Description

NCBI Mouse Build 36 data with best available position and source.

Usage

data(build36)

Format

A data frame with 4853 observations on the following 14 variables.

ID

Order of entry returned from NCBI.

snp

Build 36 rs number.

updated

Date of last update: 12/22/2005 or 4/19/2006.

snpold

Build 32 rs number.

alleles

Target allele pair or triplet from A/C A/C/G A/G A/G/T A/T C/G C/G/T C/T G/T.

het

Heterozygosity score.

sehet

Standard error of he.

assemply

One of C57BL/6J Celera build.32. One SNP was not found in build 36 at all.

chr

Chromosome name: 1 to 19 or X

chr.pos

Chromosome position in Mb (build 36).

accession

Accession number (usually NT_nnn).

ctg.start

Base pair start of SNP.

ctg.end

Base pair end of SNP (usually same as ctg.start.

orient

Orientation as given + or reversed -.

References

http://www.ncbi.nlm.nih.gov/projects/genome/seq/NCBIContigInfo.html

Examples

data(build36)
dim(build36)

byandell/qtlview documentation built on May 13, 2019, 9:53 a.m.