Table 4 MiddRAD-seq data summary in rice and maize

Genome size (Mb)

383

2300

% of repeats in genome

39.11

85.00

GC content (%)

43.56

46.83

Expected information

 Enzyme pairs

AvaII + MspI

AvaII + MspI

 Expected RAD tag size range (bp)

460–680

500–680

 Expected no. of RAD tags

60,925

284,179

 Tags density per 100 kb

15.92

12.36

 % of tags in CDS

25.10

3.04

Observed information

 Raw reads

14,732,449

7,414,009

 Clean reads

14,146,516

7,337,556

 Observed no. of tags

66,547

290,001

 Tag average depth

212.58

25.30

 Tags per 100 kb

17.38

12.61

 Simplification ratio (%)

2.43

1.77

 % of tags in CDS

31.49

1.15

 % of tags in repeats

15.83

31.44