Table 1.
From Alignments to Two-Way Synteny Blocks
|
|
|
Human—mouse |
|
Human—rat |
|
Mouse—rat |
|---|---|---|---|---|---|---|
| # PatternHunter alignments | 2,155,195 | 2,202,096 | 14,612,360 | |||
| # Two-way anchors | 642,542 | 598,632 | 1,379,600 | |||
| 300 kb two-way synteny blocks: | ||||||
| # Blocks | 394 | 417 | 162 | |||
| # Macro-rearrangements | 340 | 344 | 123 | |||
| # Micro-rearrangements | 3,744 | 4,116 | 7,421 | |||
| # Breakpoint region re-uses | 265 | 254 | 77 | |||
| # Breakpoints per breakpoint region | H: | 1.64—1.83 | H: | 1.59—1.75 | M: | 1.46—1.73 |
| (with chromosome ends-w/o chromosome ends) | M: | 1.64—1.81 | R: | 1.59—1.74 | R: | 1.46—1.74 |
| Mean synteny block length (kb) | H: | 6,851 | H: | 6,400 | M: | 15,288 |
| M: | 6,133 | R: | 6,108 | R: | 16,348 | |
| Maximum synteny block length (kb) | H: | 79,289 | H: | 55,358 | M: | 157,726 |
| M: | 64,401 | R: | 49,813 | R: | 169,760 | |
| Total synteny block length (kb) | H: | 2,699,430 | H: | 2,668,876 | M: | 2,476,643 |
| M: | 2,416,552 | R: | 2,546,960 | R: | 2,648,380 | |
| Total synteny block length (% of genome) | H: | 89.40% | H: | 88.39% | M: | 96.10% |
| M: | 93.76% | R: | 93.64% | R: | 97.37% | |
| Mean breakpoint region length (kb) | H: | 569 | H: | 610 | M: | 254 |
| M: | 253 | R: | 393 | R: | 406 | |
| Maximum breakpoint region length (kb) | H: | 26,092 | H: | 26,110 | M: | 3,549 |
| M: | 6,469 | R: | 7,555 | R: | 4,057 | |
| Total breakpoint region length (kb) | H: | 211,214 | H: | 240,150 | M: | 36,103 |
| M: | 94,731 | R: | 155,580 | R: | 57,251 | |
| Total breakpoint region length (% of genome) | H: | 6.99% | H: | 7.95% | M: | 1.40% |
| M: | 3.68% | R: | 5.72% | R: | 2.10% | |
| 1 Mb two-way synteny blocks: | ||||||
| # Blocks | 280 | 278 | 105 | |||
| # Macro-rearrangements | 246 | 243 | 84 | |||
| # Micro-rearrangements | 4,270 | 4,796 | 8,216 | |||
| # Breakpoint region re-uses | 193 | 190 | 56 | |||
| # Breakpoints per breakpoint region | H: | 1.65—1.91 | H: | 1.64—1.91 | M: | 1.50—1.98 |
| (with chromosome ends-w/o chromosome ends) | M: | 1.65—1.89 | R: | 1.64—1.89 | R: | 1.50—2.00 |
| Mean synteny block length (kb) | H: | 9,821 | H: | 9,820 | M: | 23,876 |
| M: | 8,682 | R: | 9,265 | R: | 25,457 | |
| Maximum synteny block length (kb) | H: | 79,917 | H: | 88,198 | M: | 157,726 |
| M: | 64,954 | R: | 84,258 | R: | 169,760 | |
| Total synteny block length (kb) | H: | 2,749,840 | H: | 2,729,972 | M: | 2,507,026 |
| M: | 2,430,879 | R: | 2,575,550 | R: | 2,672,970 | |
| Total synteny block length (% of genome) | H: | 91.07% | H: | 90.41% | M: | 97.27% |
| M: | 94.32% | R: | 94.69% | R: | 98.27% | |
| Mean breakpoint region length (kb) | H: | 605 | H: | 680 | M: | 58 |
| M: | 315 | R: | 488 | R: | 393 | |
| Maximum breakpoint region length (kb) | H: | 25,096 | H: | 25,821 | M: | 3,340 |
| M: | 6,073 | R: | 43,357 | R: | 10,614 | |
| Total breakpoint region length (kb) | H: | 155,553 | H: | 172,629 | M: | 4,905 |
| M: | 81,913 | R: | 125,515 | R: | 32,994 | |
| Total breakpoint region length (% of genome) | H: | 5.15% | H: | 5.72% | M: | 0.19% |
|
|
M:
|
3.18%
|
R:
|
4.61%
|
R:
|
1.21%
|
-
The information in this table only considers two species at a time; alignments with the third species are not considered. Quantities that differ between the two species are marked with H, R, or M, to denote the separate measurements. The lengths of breakpoint regions include those between synteny blocks, and exclude those at chromosome ends.
