Table 1.

The table shows the variant numbers identified by the different methods through the different filtering steps. Note, mean raw calls per mouse is not available for P4 as GATK calls jointly over all mice. Pass QC involves filtering for olfactory genes, known Sanger variants and PASS flag from GATK

	P1	P2	P3	P4
Mean raw calls	13,775,275
Mean raw calls	66,493	71,705	74,093	NA
per mouse
Total raw calls	145,484	131,926	124,788	54,698,903
(for 53 founders)
Mean filtered	39	44	41	66
SNVs per mouse
Mean combined	111
filtered SNVs
Mean agreeing	54
SNVs
Mean pass QC	21
Total ENU mutation	1281
(for 53 founders)