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)

Huang and Khatib BMC Genomics 2010 11:711   doi:10.1186/1471-2164-11-711