Table 1.

Summary of sequencing read alignment to the reference genome

Sample	Blastocysts	Degeneratives
Paired end reads	18,377,462 × 2	20,499,571 × 2
Single end reads	17,597,407	13,770,885
Total sequenced fragments	35,974,869	34,270,456
Fragments mapped to nuclear genome	22,511,851	21,480,971
(percent mapped)	(62.6%)	(62.7%)
Uniquely mapped fragments	20,417,798	19,830,476
(percent uniquely mapped)	(90.7%)	(92.3%)
Fragments mapped to mitochondrial genome	3,690,752	2,188,146
Fragments mapped to annotated junctions	2,174,923	1,268,315
(number of junctions)	(65,743)	(62,788)
Fragments mapped to putative novel junctions	129,851	84,600
(number of junctions supported by at least 2 fragments)	(10,638)	(8,686)
Fragments mapped to annotated exons	11,596,019	7,103,823
Fragments overlapped with annotated introns	2,525,630	3,644,395
Fragments mapped to annotated genes (exons + introns)	14,121,649	10,748,218
Fraction of intronic fragments among genic fragments	17.9%	33.9%
PolyA containing reads	534,090	862,915
Mapped polyA reads (with polyA signal)	112,170	120,552
(number of putative polyA sites)	(11,389)	(15,493)