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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.