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In collaboration with Doreen Ware (CSHL), Jer-Ming Chia (CSHL) and George Grills (Cornell), we (Mike Gore, Rob Elshire, Elhan Ersoz, and Jason Peiffer) are developing a maize HapMap for the 27 founder lines of NAM. We will provide more details in the next couple weeks, and the main data resource will be Panzea once the data releases stabilize (B73-Mo17 SNPs are there currently). Here are nearly half a million SNPs that follow within these criteria (about 14% of the total scored): - Scored in >12 lines. LOD genotypic score of >2.
- π diversity >0.2
- No known SNP with 10bp.
- B73 score agrees with the reference genome sequencing
- Only SNP polymorphisms (no indels)
- A filter against potential SNPs involving paralogues.
These SNPs are available for use in designing a public maize SNP array. Please do not use this data for a full genome analysis, as Mike Gore is writing paper for his dissertation on these results. Chromosome: 1 2 3 4 5 6 7 8 9 10 The header for these files is here. B73 B97 CML103 CML228 CML247 CML277 CML322 CML333 CML52 CML69 HP301 IL14H KI11 KI3 KY21 M162W M37W MO17 MO18W MS71 NC350 NC358 OH43 OH7B P39 TX303 TZI8
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