Cow vs American bison LastZ results
Cow (Bos taurus, ARS-UCD1.3) and American bison (Bison bison bison, Bison_UMD1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 111. Cow was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Masking count (M) | |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Cow | American bison |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | 10,100,000 |
| Masking options |
Statistics over 388,096 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Cow |
Uncovered: 114,612,113 out of 2,711,209,831 |
Uncovered: 357,807 out of 37,648,360 |
| American bison |
Uncovered: 406,383,603 out of 2,953,622,319 |
Uncovered: 512,377 out of 30,104,366 |
Block size distribution
| Size range | All 388,096 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 3,188 |
20.6 kb |
|||
| 10 bp - 100 bp | 27,231 |
1.4 Mb |
7,457 |
450.5 kb |
|
| 100 bp - 1 kb | 91,728 |
42.1 Mb |
21,833 |
8.2 Mb |
|
| 1 kb - 10 kb | 182,629 |
732.8 Mb |
11,403 |
41.4 Mb |
|
| 10 kb - 100 kb | 83,223 |
1.8 Gb |
7,515 |
164.1 Mb |
|
| 100 kb - 1 Mb | 97 |
11.1 Mb |
359 |
117.1 Mb |
|
| 1 Mb - 10 Mb | 351 |
1.4 Gb |
|||
| 10 Mb - 100 Mb | 61 |
890.7 Mb |
|||