## Description

This track shows simple differences between chimp alignments and the $organism assembly within regions of high quality chimp sequence. The chimp data was obtained from the 13 Nov. 2003 Arachne assembly. A total of 28,889,041 differences are displayed. The difference rate in coding sequence is approximately half that of the chimp genome as a whole.

## Methods

For a difference to be included in this track, it had to meet the following criteria:

- the difference must occur at a base of quality 30 or better
- all bases within an 11-base window around this base must have a quality of 25 or better
- the 11-base window must contain no more than two base differences
- no insertions or deletions may be present within the window

Only reciprocal best chimp alignments were considered for this track (see the Chimp Net description for more information about this alignment strategy).

## Credits

This track was generated at UCSC by Jim Kent.

The chimp sequence was obtained from the 13 Nov. 2003 Arachne assembly. We'd like to thank the National Human Genome Research Institute (NHGRI), the Broad Institute, and Washington University School of Medicine in St. Louis for providing this sequence.