Development of Genome-Wide Insertion and Deletion Polymorphism Markers from Next-Generation Sequencing Data in Rice

Rice

Table 1 Distribution of the primers and InDels in various genomic regions

Genome Region	Total Primer^a	Unique Primer^b			Unique Primer Set^c	InDel^d			Highly Polymorphic INDEL^e
Genome Region	Count	Count	Density^f	Proportion (%)^g	Count	Count	Density^f	Proportion (%)^h	Count	Density^f	Proportion (%)ⁱ
TSS_up_0.5 kb	1,372,500	659,382	23.63	48.04	655,277	227,877	8.17	34.78	17,555	0.63	2.68
5′-UTR	424,611	225,331	26.66	53.07	223,737	72,931	8.63	32.60	6061	0.72	2.71
3′-UTR	562,748	435,385	27.64	77.37	435,014	104,248	6.62	23.96	6295	0.40	1.45
CDS	3,844,531	1,545,879	17.48	40.21	1,536,689	158,448	1.79	10.31	4640	0.05	0.30
Intron	3,571,402	2,106,294	39.90	58.98	2,101,227	483,308	9.16	23.00	33,985	0.64	1.62
TES_down_0.5 kb	1,329,621	643,369	23.06	48.39	641,322	192,099	6.89	29.95	13,883	0.50	2.16
Intergenic	7,738,481	3,560,733	23.42	46.01	3,542,446	1,130,446	7.44	31.91	82,495	0.54	2.33
Total	18,662,247	8,995,927	24.10	48.20	8,955,862	2,329,724	6.24	26.01	162,380	0.44	1.81

^aTotal primers in various genomic regions
^bPrimer pairs simultaneously mapped to unique genomic regions in both Nipponbare and 9311
^cA set of unique primers with the e-PCR products in twenty or more than twenty rice genomes
^dInDels with PIC > 0
^eInDels with PIC ≥ 0.5
^fDensity was defined as the corresponding primer or InDel number every 1000 bp
^gProportion of unique primers in the total primers
^hProportion of InDels in the unique primer set
ⁱProportion of highly polymorphic InDels in the unique primer set