Table 3 Analysis of 8 clusters from hierarchical cluster analysis, including the numbers of sites from each call set and a description of the predominant types of sites in each cluster
From: svclassify: a method to establish benchmark structural variant calls
Cluster | 4000 Random | Personalis Random | Random LINEs | Random LTRs | Random SINEs | Personalis deletions | 1000 Genomes deletions | Total | Proportion that are deletions | Description |
|---|---|---|---|---|---|---|---|---|---|---|
1 | 0 | 0 | 0 | 0 | 0 | 371 | 284 | 655 | 1.000 | Mostly large, true homozygous deletions |
2 | 0 | 0 | 0 | 0 | 2 | 432 | 237 | 671 | 0.997 | Heterozygous Alu deletions |
3 | 1 | 1 | 1 | 0 | 0 | 705 | 402 | 1110 | 0.997 | Homozygous Alu deletions |
4 | 2397 | 455 | 38 | 28 | 16 | 9 | 28 | 2971 | 0.012 | Large, likely non-SVs. Generally in easy-to-sequence regions |
5 | 1073 | 1351 | 352 | 378 | 279 | 1 | 33 | 3467 | 0.010 | Smaller, likely non-SVs. Generally in easy-to-sequence regions |
6 | 17 | 2 | 1 | 0 | 0 | 3 | 138 | 161 | 0.876 | Likely true large homozygous deletions with inaccurate breakpoints so that the true deletion is larger than the called region |
7 | 14 | 16 | 2 | 2 | 4 | 624 | 811 | 1473 | 0.974 | Mostly true heterozygous deletions in easier-to-sequence regions |
8 | 498 | 481 | 103 | 90 | 195 | 161 | 752 | 2280 | 0.400 | Mix of non-SVs and SVs in more difficult regions with coverage between the normal coverage and half the normal coverage |
Total | 4000 | 2306 | 497 | 498 | 496 | 2306 | 2685 | 12788 | 0.390 | Â |