Table 3.

Categorization and abundance of clean tags.

Summary	Inoculation	Control
Clean tags
Total number	4,847,568	4,883,691
Distinct tag number	446,284	423,464
All tag mapping to genes
Total number	2,974,532	2,826,151
Total % of clean tag	61.36%	57.88%
Distinct number	95,633	82,429
Distinct tag % of clean tag	21.43%	18.81%
One tag mapping to unique genes
Total number	639,019	610,306
Distinct number	72,812	64,815
One tag mapping to multiple genes
Total number	1,996,930	1,902,489
Distinct number	85,308	75,512
Unknown tags
Total number	1,376,922	1,532,237
Total % of clean tag	28.40%	31.37%
Distinct number	288,186	283,137
Distinct tag % of clean tag	64.57%	66.86%