Table 2 Enrichment analysis of Y-linked scaffolds using hypergeometric test in R.

From: Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

Chromosome

Scaffold

Length (bp)

Total number of fragments (M)

Number of fragments (Ri-norm < 0.3)(k)

P-value (Ri-norm < 0.3)

Y-linked scaffolds

Sca971

45,330

28

18

2.166655e-44

Sca704

113,872

48

31

1.183675e-75

Sca713

110,109

52

30

5.078515e-71

Sca811

76,694

41

28

1.534825e-69

Sca3194

8,996

7

6

8.634194e-17

Sca28791

1,242

2

2

2.321559e-06

Autosomal-linked scaffold (control)

Sca667

136,669

78

2

6.4566e-3

Sca641

143,109

58

2

3.626282e-3

  1. Note: Number of total fragments in the genome reference (N) is 605,448; Number of total number of fragments (Ri-norm < 0.3) in the genome reference (n) is 923. Putative autosome scaffolds are used as controls.
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