Most of our SNP discovery efforts in C. briggsae make use of the ssaha-SNP program developed by Jim Mullikin (with A. Spargo and Z. Ning). Today I used a companion script, parse_indel, to extract insertion-deletion polymorphisms detected in 13,632 HK104 shotgun reads. For the reference sequence, I used the "cb3" assembly now available on Wormbase (L. Hillier and R. Waterston).

When I combined results from all reads, some 7,537 unique indel loci were detected. There were 306 observed in multiple reads, of which 7 were discordant (and tossed). That left me with 7,530 candidate insertion-deletion variants. Around two-thirds of these (4686) were deletions; the remaining third (2844) were insertions. This is most likely not due to biology, but due to the higher probability for detecting deletions in shotgun sequence data than insertions.

Looking at the distribution of indel sizes:
5,906 indels were 1-2 bp
1,338 indels were 3-10 bp
214 indels were 11-20 bp
72 indels were >20 bp

I hope to do some more processing (providing flanking sequence, filtering by size, etc) before making these available on the C. briggsae data downloads page.

The SNP Research Facility, headed by Dr. Raymond D. Miller (Department of Genetics) at Washington University School of Medicine, studies patterns of genetic variation in humans and model organisms. We perform high-throughput SNP genotyping using the FP-TDI platform from PerkinElmer. Our laboratory, along with Pui Kwok's group at UCSF, served as a major genotyping center for Phase I of the International HapMap Project. Currently, we are funded to develop a high-density genetic map and ancillary resources to support C. briggsae as a model organism.

This blog was launched in March of 2007 to share news, data, and perspectives related to our research.