Table 1.

Summary of small RNA next generation sequencing data processing

Processing steps	Root	Leaf	Flower	Seed	Total
Input
Unique reads	6,755,739	6,901,052	8,538,019	5,798,159	22,829,317
Total reads	23,852,494	24,059,282	23,741,532	25,494,472	97,147,780
After removing adaptors and poly-A/T/C/G/N
Unique reads	5,787,223	5,802,483	7,347,504	4,856,499	19,207,362
Total reads	20,618,934	20,514,477	20,496,815	22,312,078	83,942,304
After filtering out reads with low counts
Unique reads	1,193,873	1,161,516	1,231,736	1,079,437	1,697,668
Total reads	15,463,951	15,293,812	13,668,993	18,097,032	62,523,788
After removal of virus/chloroplast sequences (reads entered into the annotation pipeline)
Unique reads	1,164,475	1,117,720	1,206,840	1,047,951	1,649,996
Total reads	15,117,306	13,507,134	13,408,510	17,354,424	59,387,374