Table 1. Annotated SNPs and indels segregating among the eight CC/DO founder strains.

	Genome			Transcriptome
Strain	SNPs	Insertions	Deletions	SNPs	Insertions	Deletions
A/J	4,198,324	401,264	422,424	104,358	7,846	8,394
129S1/SvImJ	4,458,004	428,081	458,055	109,598	8,154	8,875
NOD/ShiLtJ	4,323,530	389,285	407,801	108,881	7,599	8,168
NZO/HILtJ	4,492,372	396,393	410,118	108,026	7,551	7,905
CAST/EiJ	17,673,726	1,359,607	1,367,482	410,805	26,975	27,474
PWK/PhJ	17,202,436	1,247,627	1,388,258	411,647	25,226	27,842
WSB/EiJ	6,045,573	588,061	608,945	146,495	10,966	11,559
All strains	31,593,523	2,963,385	3,213,340	746,993	56,354	61,204

For each of the founder strains, the cumulative numbers of high-quality SNPs, insertions, and deletions that differ from the NCBIM37 genome and transcriptome are listed. Transcript boundaries are based on the Ensembl v67 annotation. The bottom row tabulates the total number of variants segregating among the founder strains that differ from NCBIM37.