Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data

BMC Genomics

Table 1 Distribution of e-PCR primers and polymorphic indels in different regions of the maize genome

Genome region	Total^a	Unique Primer^b			Indel^c (PIC > 0)			High polymorphic indel (PIC ≥ 0.5)
Genome region	Total^a	Count	Density^d (Kb)	Rate^e (%)	Count	Density (Kb)	Rate^f (%)	Count	Density (Kb)	Rate^g (%)
TSS_up_0.5Kb	978,913	519935	26.27	53.11	135326	6.84	27.76	20419	1.03	4.19
5’-UTR	614,397	352736	11.62	57.41	88155	2.90	25.86	13294	0.44	3.90
3'-UTR	614,453	352784	11.61	57.41	88166	2.90	25.86	13297	0.44	3.90
CDS	2,204,900	1025151	16.29	46.49	77294	1.23	7.89	7272	0.12	0.74
Intron	5,081,799	2050762	11.99	40.36	389605	2.28	19.60	54527	0.32	2.74
TES_down_0.5Kb	967,784	488116	24.66	50.44	116096	5.87	25.17	16589	0.84	3.60
Intergenic	93,492,302	7569844	4.08	8.10	1206314	0.65	18.56	157841	0.08	2.43
Total^h	102,929,122	11807240	5.74	11.47	1973746	0.96	18.68	264214	0.13	2.50

^aAll primers on the whole 10 chromosomes
^bPrimers were located in unique genomic region
^cPolymorphism primers were primers with length information in 20 or more than 20 genomes and PIC Value >0
^dDensity was calculated by number/Kb
^eThis rate was the percentage of unique primer against overall primer
^fThis rate was the percentage of unique primer with polymorphisms against unique primer
^gThis rate was the percentage of unique primer with polymorphisms greater than or equal to 0.5 against unique primer
^hThere were 102,929,122 primers in total, and the same primer might be divided into different regions and double counting due to the alternative splicing occurring in maize genome

ISSN: 1471-2164