Table 1.

Summary of sequence read alignments to the reference genome

Sample	In vitro embryos	In vivo embryos
Pair end reads	26,906,451 x 2	38,184,547 x2
Total sequenced fragments	26,906,451	38,184,547
Total mapped fragments	22,428,488	32,384,577
Uniquely mapped fragments	20,389,330	29,728,363
Fragments mapped to autosomes and X chromosome	19,556,926	28,362,794
Fragments mapped to annotated genes	13,304,981	16,976,922
Fragments mapped to annotated exons	6,942,761	8,185,094
Fragments overlapped with annotated introns	6,362,220	8,791,828