Table 1. Analysis of sequence artifacts.

	Unfiltered Error Rate (Fig. 2 Animals)		Filtered Error Rate (Fig. 2 Animals)		Filtered Error Rate (Whole Cohort)
	# Reads	(%)	# Reads	(%)	# Reads	(%)
Total High Quality Reads	21,950		21,950		484,985
Failed Assembly	NA		1,548	(7.1)	73,114	(15.1)
Passed Assembly	NA		20,402	(92.9)	411,871	(84.9)
Total Reads for Error Analysis	21,950		20,402		411,871
MHC Class I	20,497	(93.4)	20,050	(98.3)	406,274	(98.5)
Insertions/Deletions	762	(3.5)	300	(1.5)	2,914	(0.8)
Single Base Substitutions	321	(1.5)	22	(0.1)	565	(0.1)
Multiple Base Substitutions	124	(0.6)	30	(0.1)	2,118	(0.5)
Short Reads (<180bp)	246	(1.1)	0	(0)	0	(0)