Table 1 RNA-Seq reads mapped backed to the maize genome (5a.59)

Percentage of reads mapped back to nuclear genome

82%

85%

61%

81%

nd

nd

Total mapped reads

91,076,832

123,536,281

50,435,150

140,282,423

nd

nd

Reads mapped to FGS low-copy exons

46,765,091

100,723,578

34,727,288

117,425,717

17,569,670

16,837,249

Reads mapped to RGS Low-copy exons

2,099,557

1,822,553

1,602,788

3,873,497

Intron

3,214,112

367,752

1,110,429

2,277,426

nd

nd

Intergenic

1,522,581

2,732,794

5,583,100

4,199,131

nd

nd

Ribosomal RNA genes

21,039,136

4,306,489

729,102

4,224,584

nd

nd

Transposons and other repeats

8,256,280

12,504,295

3,590,804

3,629,696

nd

nd

Mitochondrial genes

3,442,450

49,613

1,399,727

2,450,967

nd

nd

Chloroplast genes

4,176,008

771

988,470

1,592,112

nd

nd

Genes in FGS with average expression > 0.1 FPKM (39,635 total)

27,564

14,591

27,530

25,971

20,857

20,539

Genes in RGS with average expression > 0.1 FPKM (69,689 total)

8,165

4,335

17,751

11,933

nd

nd

Percentage of FGS Expressed Genes (>0.1 FPKM) in only one replicate

9%

18%

16%

11%

19%

9%

Percentage of FGS Expressed Genes (>0.1 FPKM) in two replicates

8%

13%

17%

8%

15%

14%

Percentage of FGS Expressed Genes (>0.1 FPKM) in all Three Replicates

83%

69%

67%

81%

66%

77%