Table 2 CNV regions from 50 CNVs of three detection algorithms in comparison with recent studies
ECA | CNV regions detected by CNVPartition, PennCNV, QuantiSNP (717 horses) (bp) | CN | Samples (n) | CNV regions detected by PennCNV (477 horses); Dupuis et al.(bp) | CN | Samples (n) | CNV regions detected CGH analysis (16 horses); Doan et al.(bp) | CN | Samples (n) |
|---|---|---|---|---|---|---|---|---|---|
1 | 155487276-155656642 | Loss, gain | 162, 13 | 155487276-155656642 | Loss | 78 | 155360077–155640397 | Loss, gain | 3 |
|  |  |  |  |  |  |  | 155905880–155936772 | Loss | 1 |
|  |  |  |  |  |  |  | 155936817–155937275 | Gain | 2 |
|  |  |  |  |  |  |  | 155972933–155973160 | Gain | 1 |
|  |  |  |  |  |  |  | 156313490–156314132 | Loss | 1 |
|  |  |  |  |  |  |  | 156657191–156690829 | Loss | 1 |
|  |  |  |  |  |  |  | 156690978–156714131 | Gain | 6 |
1 | 178798269- 179550475 | Loss, gain | 10, 5 | 178798269-178815370 | Loss | 1 | ─ |  |  |
| Â | Â | Â | 178798269-179550475 | Gain | 3 | Â | Â | Â | |
2 | 106062109-106063373 | Gain | 20 | 106062109-106064917 | Loss | 7 | ─ |  |  |
3 | 65705932- 65951800 | Loss, gain | 27, 29 | 65705932-66065643 | Gain | 50 | ─ |  |  |
4 | 52424614-52612016 | Gain | 20 | 52194368-52612016 | Gain | 1 | ─ |  |  |
5 | 37840041-37916448 | Loss | 16 | 37840041-37916448 | Loss | 5 | 37878731-37954286 | Loss, gain | 9, 8 |
5 | 88243192-88258862 | Gain | 57 | 88243192-88349479 | Gain | 27 | ─ |  |  |
6 | 26086675-26126581 | Gain | 42 | 26102028-26126581 | Gain | 1 | ─ |  |  |
6 | 72032729-72607543 | Loss, gain | 136, 11 | 71956823-72607543 | Loss | 71 | 71977669-73390784 | Loss, gain | 5, 1 |
7 | 31406445-31520977 | Loss | 17 | 31406445-31529855 | Loss | 10 | ─ |  |  |
7 | 52610482-52677786 | Gain | 37 | 52610482-52677786 | Gain | 39 | 52617898-52737112 | Loss, gain | 5 ,4 |
7 | 73083306-73197149 | Loss, gain | 14, 3 | 73083306-73197149 | Loss | 3 | 73056824-73699458 | Loss, gain | 14, 14 |
8 | 4280605-4621044 | Loss, gain | 37, 40 | 4183178-4430473 | Loss | 2 | 4381193-4648028 | Gain | 2 |
9 | 31574454-31574969 | Loss | 4 | ─ | ─ | ─ | ─ |  |  |
10 | 674485-1271225 | Loss, gain | 1, 6 | 674485-1141923 | Gain | 10 | ─ |  |  |
11 | 54645681-54812394 | Loss | 47 | 54640169-54812394 | Loss | 1 | ─ |  |  |
12 | 12524489-14777981 | Loss, gain | 108, 116 | 12524489-13488187 | Loss | 32 | 12314908-15866355 | Loss, gain | 12, 13 |
| Â | Â | Â | 13945011-14777981 | Loss | 114 | Â | Â | Â | |
18 | 11660478-12399073 | Gain | 2 | ─ | ─ | ─ | ─ |  |  |
20 | 32059082-32210308 | Loss, gain | 24, 3 | 32059082-32250493 | Gain | 9 | 32031829-32033708 | Loss | 1 |
24 | 32416012-32628728 | Loss, gain | 1, 11 | 32416012-32628728 | Gain | 20 | ─ |  |  |
25 | 26318531-27125754 | Loss, gain | 137, 4 | 26318531-26942120 | Loss | 99 | 26274719-26980393 | Loss, gain | 2, 2 |