Mouse vs Eurasian red squirrel LastZ results
Mouse (Mus musculus, GRCm39) and Eurasian red squirrel (Sciurus vulgaris, mSciVul1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 103. Mouse 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 | Mouse | Eurasian red squirrel |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,568,638 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,705,180,188 out of 2,728,222,451 |
Uncovered: 936,627 out of 36,014,121 |
| Eurasian red squirrel |
Uncovered: 1,884,333,720 out of 2,878,591,032 |
Uncovered: 2,620,454 out of 33,947,064 |
Block size distribution
| Size range | All 1,568,638 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 22,124 |
147.2 kb |
|||
| 10 bp - 100 bp | 165,695 |
9.3 Mb |
35,513 |
2.4 Mb |
|
| 100 bp - 1 kb | 1,018,831 |
466.5 Mb |
89,920 |
29.9 Mb |
|
| 1 kb - 10 kb | 361,631 |
635.5 Mb |
17,932 |
40.0 Mb |
|
| 10 kb - 100 kb | 347 |
5.6 Mb |
535 |
14.3 Mb |
|
| 100 kb - 1 Mb | 10 |
1.2 Mb |
123 |
42.1 Mb |
|
| 1 Mb - 10 Mb | 116 |
413.6 Mb |
|||
| 10 Mb - 100 Mb | 33 |
575.9 Mb |
|||