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Table 3 Comparison between 754 CNV regions detected by CGH analyses and the SNP array detection results of CNVPartition, PennCNV and QuantiSNP

From: Analysis of copy number variants by three detection algorithms and their association with body size in horses

ECA Number of CNV regions detected CGH analysis, Doan et al.(n) CNV regions detected by CNVPartition (%) CNV regions detected by PennCNV (%) CNV regions detected by QuantiSNP (%)
1 67 11 11 24
2 31 3 3 35
3 35 0 3 29
4 27 7 11 15
5 44 0 0 11
6 29 7 4 14
7 50 2 4 12
8 24 4 4 38
9 17 0 6 29
10 31 0 0 48
11 39 3 5 28
12 15 7 13 47
13 22 0 55 55
14 32 0 3 34
15 33 0 0 3
16 23 0 0 13
17 22 0 5 14
18 27 0 0 19
19 14 0 0 0
20 47 4 9 17
21 18 0 0 33
22 21 0 0 29
23 17 6 6 24
24 10 0 0 0
25 14 29 29 43
26 4 0 0 0
27 7 0 57 86
28 5 0 100 80
29 6 17 0 17
30 14 0 0 50
31 9 0 0 0
total 754 3 7 25
  1. All CNV regions that show an overlap of at least 50% with the CNV region detected by CGH are displayed for each chromosome. The highest overlap can be seen with QuantiSNP.