Single Feature Polymorphisms

Single Feature Polymorphisms

New Full Genome DATA 10/21/03!!!

See Methods paper for the latest scripts

eXtreme Array Mapping for QTL

This page contains data, scripts, tables and addition figures for

Large Scale Identification of Single Feature Polymorphisms in Complex Genomes


Justin O. Borevitz, David Liang, David Plouffe, Hur-Song Chang, Tong Zhu, Detlef Weigel,

Charles C. Berry, Elizabeth Winzeler, Joanne Chory

Supplementary data

Current DNA labeling protocol here

A link to a graphical genome browser showing all the features and which ones are markers

Search At4g10780 as an example and zoom in.

Perl scripts for finding unique features in the genome and mini-micro satellites are in (fixed 5/8/2004)

A table of all 92924 features and which are markers in Ler, Ws-2, Nd-1, Tsu-1, and Cvi

Large .pdf files of deletions across the genome. Ler, Ws-2, Nd-1, Tsu-1, and Cvi

Let’s get started with the analysis in R (download R)

A link to lcluster R library for calling deletions

A link to bqtl R library that assists ChipMap

Download the setup files.

Follow the readme.txt file in

You can get the 3 Col and 3 Ler .cel files for AtGenome1 here

You can read the data in, identify SFPs, set permutation threshold,

and confirm SFPs with sequence data, etc. Then do the clustering to identify deletions

Here are the .cel files for accessions (Ws-2,Nd-1,Tsu,and Cvi) and for mapping.

Finally do some mapping.

Enjoy Justin Borevitz & Charles Berry