Table 1.

Summary of sequence read alignments to the reference genome

Sample	In vivo derived embryos (mean ± SD)	Serum-free produced embryos (mean ± SD)	Serum-containing produced embryos (mean ± SD)
Paired end reads	14701822.4 ± 1066098.2 × 2	12731192.8 ± 615768.7 × 2	14670296.3 ± 2890016 × 2
Total sequenced fragments	14701822.4 ± 1066098.2	12731192.8 ± 615768.7	14670296.3 ± 2890016
Total mapped fragments	7508158 ± 709020.2	6636857.8 ± 552752.8	7240822.8 ± 2076161.5
Uniquely mapped fragments	7028287.1 ± 662984.5	6174226.4 ± 523270.2	6691366.4 ± 1939025.2
Fragments mapped to annotated genes	7028287.1 ± 662984.5	6174226.4 ± 523270.2	6691366.4 ± 1939025.2
Fragments mapped to annotated exons	4353683.6 ± 619988.6	4119767.6 ± 760316.3	4730978.5 ± 1683623.3
Fragments overlapped with annotated introns	2674603.5 ± 157817.1	2054458.8 ± 430089.5	1960387.9 ± 465486.1

The numbers correspond to the mean ± standard deviation (SD) of all the replicates per condition