Table 4.
Four-way human-mouse-rat-chicken synteny blocks based on sequence alignments
|
|
Human |
Mouse |
Rat |
Chicken |
|---|---|---|---|---|
| Chromosomes included | 1–22, X | 1–19, X | 1–20, X | 1–24, 26–28, 32, W, Z |
| Total length (Mb) | 3020 | 2577 | 2720 | 940 |
| Run 100K | ||||
| No. of blocks | 583 | 583 | 583 | 583 |
| Mean synteny block length (kb) | 2713 | 2436 | 2566 | 1083 |
| Max synteny block length (kb) | 44,708 | 38,350 | 41,531 | 16,085 |
| Total synteny block length (kb) | 1,581,616 | 1,420,395 | 1,495,964 | 631,341 |
| Total synteny block length (% of genome) | 52.37% | 55.11% | 55.00% | 67.15% |
| No. of breakpoint regions | 560 | 563 | 562 | 553 |
| Mean breakpoint region length (kb) | 2254 | 1815 | 2065 | 509 |
| Max breakpoint region length (kb) | 40,507 | 19,233 | 33,229 | 5247 |
| Total breakpoint region length (kb) | 1,262,211 | 1,021,678 | 1,160,670 | 281,338 |
| Total breakpoint region length (% of genome) | 41.80% | 39.64% | 42.67% | 29.92% |
| No. of anchors per block | 5–2915, mean 234.2 | |||
| Run 200K | ||||
| No. of blocks | 474 | 474 | 474 | 474 |
| Mean synteny block length (kb) | 3556 | 3191 | 3365 | 1409 |
| Max synteny block length (kb) | 44,292 | 38,350 | 41,501 | 16,085 |
| Total synteny block length (kb) | 1,685,370 | 1,512,364 | 1,595,170 | 667,927 |
| Total synteny block length (% of genome) | 55.81% | 58.68% | 58.65% | 71.04% |
| No. of breakpoint regions | 451 | 454 | 453 | 444 |
| Mean breakpoint region length (kb) | 2534 | 2034 | 2316 | 550 |
| Max breakpoint region length (kb) | 46,565 | 14,435 | 32,219 | 7563 |
| Total breakpoint region length (kb) | 1,142,700 | 923,594 | 1,049,169 | 244,138 |
| Total breakpoint region length (% of genome) | 37.84% | 35.84% | 38.57% | 25.97% |
| No. of anchors per block | 11–3213, mean 319.6 | |||
| Run 300K | ||||
| No. of blocks | 430 | 430 | 430 | 430 |
| Mean synteny block length (kb) | 4049 | 3620 | 3814 | 1596 |
| Max synteny block length (kb) | 45,607 | 38,350 | 42,466 | 16,085 |
| Total synteny block length (kb) | 1,740,889 | 1,556,569 | 1,639,876 | 686,262 |
| Total synteny block length (% of genome) | 57.65% | 60.40% | 60.29% | 72.99% |
| No. of breakpoint regions | 407 | 410 | 409 | 400 |
| Mean breakpoint region length (kb) | 2662 | 2136 | 2451 | 562 |
| Max breakpoint region length (kb) | 44,269 | 15,587 | 32,219 | 10,187 |
| Total breakpoint region length (kb) | 1,083,594 | 875,902 | 1,002,423 | 224,812 |
| Total breakpoint region length (% of genome) | 35.88% | 33.99% | 36.85% | 23.91% |
| No. of anchors per block
|
16–3410, mean 370.6
|
|
|
|
-
Several sets of four-way synteny blocks were formed from sequence alignments at different resolutions. “100K” blocks must be at least 100 kb in each species and allow for anchors to be displaced up to 100 kb in a certain metric, as explained in the text under “GRIMM-Synteny parameters.” Statistics are shown on the sizes of the blocks and the breakpoint regions between them (excluding chromosome ends).
