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

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

Genome Region Total Primera Unique Primerb Unique Primer Setc InDeld Highly Polymorphic INDELe
Count Count Densityf Proportion (%)g Count Count Densityf Proportion (%)h Count Densityf 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
  1. aTotal primers in various genomic regions
  2. bPrimer pairs simultaneously mapped to unique genomic regions in both Nipponbare and 9311
  3. cA set of unique primers with the e-PCR products in twenty or more than twenty rice genomes
  4. dInDels with PIC > 0
  5. eInDels with PIC ≥ 0.5
  6. fDensity was defined as the corresponding primer or InDel number every 1000 bp
  7. gProportion of unique primers in the total primers
  8. hProportion of InDels in the unique primer set
  9. iProportion of highly polymorphic InDels in the unique primer set