Table 1.

RRBS sequencing depth for each sample

Mouse strain	Treatment	Batch	# of reads 100bp/read	# of mapped reads	# of reads after QC*	Mapability
BALB/cJ	Control	Batch 1	196,132,876	108,834,401	108,172,874	55.15%
BALB/cJ	ISO	Batch 1	190,915,791	113,543,242	112,792,817	59.08%
BUB/BnJ	Control	Batch 1	209,747,249	105,732,683	105,046,961	50.08%
BUB/BnJ	ISO	Batch 1	182,087,726	101,999,903	100,609,652	55.25%
BALB/cJ	Control	Batch 2	83,224,678	43,990,632	43,989,246	52.86%
BALB/cJ	ISO	Batch 2	89,028,320	46,538,221	46,536,900	52.27%
BUB/BnJ	Control	Batch 2	90,112,603	47,023,872	47,022,943	52.18%
BUB/BnJ	ISO	Batch 2	87,836,780	47,242,872	47,241,990	53.78%
BALB/cJ	Control	Batch 3	26,750,907	13,599,388	13,587,484	50.79%
BALB/cJ	ISO	Batch 3	24,447,253	14,831,117	14,829,851	60.66%
BUB/BnJ	Control	Batch 3	29,104,605	16,941,795	16,939,936	58.20%
BUB/BnJ	ISO	Batch 3	28,631,652	18,342,525	18,342,070	64.06%

^*Reads not fully converted by bisulfite treatment were removed, as indicated by an XS=1 tag in the output of BS Seeker2.