Table 1. Six categories of generated miRNA sequences.

Category	Group		Sequence
Reads mapped to selected pre-miRNAs in miRbase	Group 1	Group 1a	Mapped to Gallus gallus known pre-miRNAs
		Group 1b	Mapped to mammalian known pre-miRNAs which could be mapped to Gallus gallus genome
	Group 2	Group 2a	Mapped to mammalian known pre-miRNAs which could not be mapped Gallus gallus genome, but reads mapped to Gallus gallus genome and within hairpins
		Group 2b	Mapped to mammalian known pre-miRNAs which unmapped to Gallus gallus genome, but reads mapped to Gallus gallus genome, no hairpins.
	Group3	Group 3a	Mapped to mammalian known pre-miRNAs which unmapped to Gallus gallus genome, reads unmapped to Gallus gallus genome, but reads mapped to mature miRNAs.
		Group 3b	Mapped to mammalian known pre-miRNAs which unmapped to Gallus gallus genome, reads unmapped to Gallus gallus genome, but reads unmapped to mature miRNAs.
Reads unmapped to selected mirs in miRbase	Group4	Group 4a	Unmapped to known miRNAs but mapped to Gallus gallus genome and within hairpins
		Group 4b	Unmapped to known miRNAs but mapped to Gallus gallus genome and without hairpins
	Group 5	others	Mapped to other defined databases, such as mRNA, RFam, or Repbase
	Group6	No hit	None of the above