The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data

Table 2 Distribution of e-PCR primer and polymorphic indels in different regions of the cucumber genome

Genome Region	Total	Unique Primer^a	InDels ^b (PIC>0)			High polymorphicInDel(PIC ≥ 0.5)
Genome Region	Total	Unique Primer^a	Count	Density^c (number/kp)	Rate^d (%)	Count	Density (number/kp)	Rate^e (%)
TSS_up_0.5 kb	53,199,600	589,796	163,160	3.07	27.66	7,522	12.75	1.28
5’UTR	3,357,940	156,913	31,836	9.48	20.29	1,585	10.10	1.01
3’UTR	5,603,815	278,243	54,050	9.65	19.43	2,336	8.40	0.84
CDS	5,603,815	1,585,140	312,348	8.23	19.70	1,902	1.20	0.12
Intron	43,955,360	2,197,768	268,875	6.12	12.23	13,685	6.23	0.62
TES_down_0.5 kb	28,209,168	605,347	109,337	3.88	18.06	7,438	12.29	1.23
Intergenic	123,470,359	3,953,671	815,854	6.61	20.64	53,228	13.46	1.35
Total^f	295,728,002	8,953,755	1,675,641	5.67	18.71	86,301	9.64	0.96

a. Primers were located in unique genomic region
b. Polymorphisms primers were primers with length information in twenty or more than twenty genomes and PIC Value > 0
c. Density was calculated by number/Kp
d. This rate was the percentage of unique primer against overall unique primer
e. This rate was the percentage of unique primer with polymorphisms greater than or equal to 0.5 against unique primer
f. There were 7,406,619 primers in total, and the same primer might be divided into different regions and double counting due to the alternative splicing occurring in cucumber genome

ISSN: 1471-2164