Table 1. CNV call sets information on the 1000 Genomes Project WES data set.
| Chr | Number of targets (before/after QC) | CODEX | XHMM | CoNIFER | EXCAVATOR CNVs | |||
|---|---|---|---|---|---|---|---|---|
| K | CNVs | PCs | CNVs | PCs | CNVs | |||
| 1 | 15 426/14 101 | 3 | 361 (301-60) | 4 | 129 (56-73) | 36 (13-23) | 263 (236-27) | |
| 2 | 9640/8956 | 3 | 54 (14-40) | 4 | 51 (16-35) | 6 (0-6) | 15 (0-15) | |
| 3 | 8267/7775 | 3 | 13 (0-13) | 4 | 8 (0-8) | 4 (0-4) | 5 (0-5) | |
| 4 | 5519/5157 | 4 | 27 (16-11) | 4 | 20 (7-13) | 16 (6-10) | 91 (86-5) | |
| 5 | 6403/5950 | 3 | 163 (143-20) | 4 | 39 (23-16) | 5 (0-5) | 79 (72-7) | |
| 6 | 6997/6569 | 3 | 115 (95-20) | 4 | 34 (11-23) | 15 (6-9) | 62 (58-4) | |
| 7 | 6210/5546 | 3 | 164 (118-46) | 4 | 62 (24-38) | 6 (0-6) | 121 (108-13) | |
| 8 | 4477/4118 | 3 | 51 (42-9) | 4 | 12 (0-12) | 2 (0-2) | 41 (39-2) | |
| 9 | 5777/5136 | 3 | 27 (6-21) | 4 | 24 (0-24) | 7 (0-7) | 66 (42-24) | |
| 10 | 6354/5759 | 3 | 28 (6-22) | 4 | 27 (9-18) | 6 (0-6) | 55 (50-5) | |
| 11 | 7778/6979 | 3 | 77 (54-23) | 4 | 26 (0-26) | 7 (0-7) | 73 (45-28) | |
| 12 | 7817/7261 | 3 | 35 (6-29) | 4 | 32 (2-30) | 4 | 9 (0-9) | 25 (12-13) |
| 13 | 2536/2362 | 3 | 14 (0-14) | 4 | 7 (0-7) | 0 (0-0) | 3 (0-3) | |
| 14 | 4482/4127 | 3 | 37 (29-8) | 4 | 16 (0-16) | 8 (7-1) | 56 (46-10) | |
| 15 | 4635/4150 | 3 | 93 (66-27) | 4 | 40 (18-22) | 5 (0-5) | 73 (65-8) | |
| 16 | 5596/4744 | 4 | 154 (124-30) | 5 | 86 (57-29) | 9 (0-9) | 112 (78-34) | |
| 17 | 8283/7386 | 3 | 91 (58-33) | 4 | 49 (23-26) | 10 (0-10) | 124 (110-14) | |
| 18 | 2021/1888 | 3 | 4 (0-4) | 4 | 5 (0-5) | 1 (0-1) | 3 (0-3) | |
| 19 | 7438/5982 | 4 | 168 (117-51) | 5 | 135 (103-32) | 15 (0-15) | 197 (131-66) | |
| 20 | 3966/3497 | 3 | 11 (7-4) | 4 | 9 (0-9) | 1 (0-1) | 18 (7-11) | |
| 21 | 1499/1314 | 4 | 4 (0-4) | 4 | 29 (26-3) | 0 (0-0) | 61 (58-3) | |
| 22 | 2957/2493 | 4 | 79 (62-17) | 5 | 55 (38-17) | 12 (0-12) | 124 (107-17) | |
| X | 5436/4787 | 3 | 36 (15-21) | 4 | 60 (41-19) | 9 (0-9) | 248a (248a-0) | |
| Y | 281/146 | 3 | 0 (0-0) | 3 | 0 (0-0) | 0 (0-0) | 144a (144a-0) | |
| Sum | 139 795/126 183 | - | 1806 (1279-527) | - | 955 (454-501) | - | 189 (32-157) | 1667 (1350-317) |
Number of exon targets before and after QC procedure is shown. CNVs detected by CODEX, XHMM, CoNIFER and EXCAVATOR are shown and are further categorized into common and rare ones (common–rare in parentheses). Number of latent factors (K) and PCs are shown for latent factor models: default values from CODEX and XHMM are adopted; number of PCs for CoNIFER is chosen at 4 so that it is conservative by the scree plot and is comparable to XHMM.
aExcluded due to mishandling of sex chromosomes by EXCAVATOR.