Table 2.

Distribution of the unique primers and InDels on rice chromosomes

Chromosome	Chromosome length (bp)	Unique primerb		InDeld
		Count	Densityf	Count	Densityf
1	43270923	1,175,638	27.17	299,457	6.92
2	35937250	1,011,186	28.14	259,989	7.23
3	36413819	1,046,792	28.75	262,345	7.20
4	35502694	777,218	21.89	196,803	5.54
5	29958434	728,667	24.32	190,707	6.37
6	31248787	754,761	24.15	200,616	6.42
7	29697621	733,083	24.68	191,446	6.45
8	28443022	604,746	21.26	158,366	5.57
9	23012720	555,769	24.15	146,065	6.35
10	23207287	496,144	21.38	129,305	5.57
11	29021106	562,780	19.39	150,050	5.17
12	27531856	549,143	19.95	144,395	5.24
Total	373245519	8,995,927	285.24	2,329,544	74.04
Average	31103793.25	749,660.58	24.10	194,128.67	6.24

^bPrimer pairs simultaneously mapped to unique genomic regions in both Nipponbare and 9311

^dInDels with PIC > 0

^fDensity was defined as the corresponding primer or InDel number every 1000 bp