Table 3 Statistics describing the distribution of different properties of RAD sequences after each step of filtering (FASTX-Toolkit), alignment to the eel draft genome (Bowtie) and assemblage into loci (Ref_map.pl)

From: Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms

FASTX

Species

Raw reads

Filtered reads

% Eliminated

Mean Q

Q1

Med

Q3

%A

%C

%G

%T

All

8 810 898

7 281 642

17.32

38.45

37.80

39.24

40

29.8

20.5

20.1

29.6

AA

8 769 831

7 007 835

19.92

38.36

37.72

39.10

40

29.7

20.5

20.1

29.6

AR

8 851 964

7 555 450

14.72

38.53

37.88

39.37

40

29.8

20.5

20.1

29.6

Bowtie

Species

Reads

Aligned

% Aligned

Nonaligned

% Nonaligned

Discarded

% Discarded

All

7 281 642

4 707 002

64.25

2 504 043

34.15

117 695

1.60

AA

7 007 835

4 768 089

67.16

2 218 176

31.22

115 152

1.63

AR

7 555 450

4 645 915

61.33

2 789 910

37.09

120 238

1.58

Ref_map

Species

Reads

Stacks

Loci

Loci used

% Loci used

Loci discarded

% Loci discarded

All

4 707 002

663 555

322 314

214 178

66.45

108 136

33.55

AA

4 768 089

745 193

333 871

224 896

67.36

109 309

32.74

AR

4 645 915

581 918

310 756

203 638

65.53

107 118

34.47

  1. Abbreviations: AA, Anguilla anguilla; AR, A. rostrata; RAD, Restriction site Associated DNA.
Back to article page