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Table 6 The segmental repeats and interspersed repeats-included percentage of start and end regions of CNV

From: Comparative analysis of copy number variation detection methods and database construction

Programs Segmental repeats ALL* Only SINE Only LINE Only LTR Segmental repeat +interspersed repeats (ALL*)
Random*
± 500bp
2.8 17.3* 0.0 7.8 1.6 19.6
Random
± 1kbp
2.9 21.7 0.4 10.6 1.9 24.1
CNVCommon1
± 500bp
34.0 24.8 0.0 12.4 2.3 53.9
CNVCommon1
± 1kbp
34.6 39.5 1.3 21.9 5.6 62.7
CNVCommon2
± 500bp
32.2 29.1 0.0 11.6 2.5 53.7
CNVCommon2
± 1kbp
33.1 43.8 0.0 25.8 5.0 65.3
  1. ALL* means all interspersed repeats of repeatmasker 3.2.7.
  2. CNVcommon1: 315 CNV regions detected by at least two programs and more than once.
  3. CNVcommon2: 121 CNV regions detected by PennCNV more than four times (that is, at least five individuals) and at least one other program. Random*:1000 randomly extracted regions whose lengths are close to extracted CNV lengths.