Table 2. Summary of sequencing read alignments to the reference genome.

Sample	TotalReads	Total Mapped Reads	Percent Mapped	Uniquely mapped Reads	Percent uniquely mapped	Reads mapped to annotated exons
C1.1	18,683,178	14,865,139	80	13,804,648	93	7,579,921
C1.2	24,617,256	16,065,170	65	14,644,960	91	6,668,507
C2.1	16,999,297	12,754,794	75	11,670,891	92	5,624,126
C2.2	19,352,730	14,232,476	74	13,064,631	92	6,461,949
C3.1	18,158,624	13,692,675	75	12,524,307	91	7,423,716
C3.2	20,488,552	15,917,040	78	14,282,447	90	1,745,048
C4.1	17,751,765	14,181,546	80	12,937,347	91	6,066,196
C4.2	19,319,918	15,736,767	81	14,532,068	92	7,778,414
M5.1	21,048,132	16,307,207	77	14,993,073	92	7,257,007
M5.2	18,785,042	14,273,157	76	13,063,772	92	7,578,668
M6.1	21,231,578	16,546,777	78	15,056,124	91	7,339,356
M6.2	15,886,593	12,745,983	80	11,738,823	92	5,941,973
M7.1	19,294,383	14,642,903	76	13,280,140	91	7,826,542
M7.2	15,078,732	11,628,448	77	10,663,643	92	6,582,004
M8.1	18,057,137	14,080,144	78	12,768,027	91	7,184,256
M8.2	19,600,350	14,327,542	73	12,981,732	91	7,405,798

Samples belong to control (C) and methionine-rich (M) treatments, respectively. A total of 8 cows, 4 per treatment, were used. Embryos recovered from each cow were pooled in order to generate two replicates per cow assayed.