Table 1. Some identified PHAS loci of Chinese sacred lotus.

PHAS_ID	Start	End	TR	PR	P-value	FDR	P.S.	Locus Annotation	Ref.
21 nt
scaffold_106_1	375,169	376,010	94	9			15.6	putative TAS3a	[9], [11], [30]
scaffold_107_1	1,397,214	1,397,907	87	11			18.1	unknown
scaffold_10_1	1,954,273	1,954,966	88	9			12.2	putative TAS3c	[9], [11], [30]
scaffold_131_1	70,673	71,429	97	11			26.1	Putative disease resistance protein RGA3	[21]
scaffold_149_1	773,189	773,819	156	12			10.4	LSU-rRNA
scaffold_170_1	166,669	167,980	61	10			29.2	unknown
scaffold_326_1	253,709	254,360	170	13			12.9	LSU-rRNA
scaffold_326_2	254,166	254,838	58	6			11.5	LSU-rRNA
scaffold_326_3	324,761	325,370	162	12			21.2	LSU-rRNA
sf_39_1	2,038,471	2,039,238	143	12			15.9	putative TAS4	[19]
scaffold_65_1	675,292	676,027	73	10			27.0	putative TAS3b	[9], [11], [30]
scaffold_87_1	119,206	120,004	33	5			13.5	putative NB-LRR disease resistance protein	[21]
sf_88_1	539,406	540,015	101	9			13.0	LSU-rRNA
scaffold_8_1	9,281,139	9,281,769	12	6			10.8	Putative disease resistance protein RPP13	[21]
scaffold_8_2	9,353,049	9,353,721	90	12			13.6	Protein of unknown function
scaffold_90_1	1,885,970	1,886,621	25	7			10.8	putative Transcription factor MYB90	[26]
PHAS_sf_173_1	496,493	497,186	45	7			7.0	putative MYB transcription factor	[26]
PHAS_sf_21_1	1,961,563	1,962,329	81	8			7.8	putative WER, MYB transcription factor	[26]
PHAS_sf_122_1	581,162	581,771	4	4			5.6	putative NB-LRR disease resistance protein	[21]
24 nt
scaffold_24_1	6,030,639	6,031,302	82	7			10.0	intergenic region
scaffold_252_1	376,585	377,296	49	5			12.8	intergenic region
scaffold_287_1	359,861	360,500	20	5			11.2	unknown gene
scaffold_39_1	2,038,529	2,039,168	81	7			10.2	overlapped with sf_39_1
scaffold_42_1	2,581,628	2,582,459	29	4			12.7	expressed sequence match
scaffold_5_1	3,813,044	3,813,827	7	4			10.1	intron of a protein of unknown function
scaffold_88_1	1,770,018	1,770,657	96	8			15.1	unknown gene

The Start and End column list the start and end positions of the predicted PHAS loci in the scaffold. The TR and PR column list the total number of unique siRNAs and the number of phased unique siRNAs, respectively. The P-value and FDR column list the P-values evaluated with Equation 1 and the false discovery ratio using method in [35]. The P.S. column lists the phase scores calculated using Equation 2. The Ref. column lists related literature of the predicted PHAS loci.