Mouse vs Lesser Egyptian jerboa LastZ results
Mouse (Mus musculus, GRCm39) and Lesser Egyptian jerboa (Jaculus jaculus, JacJac1.0) 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 | Lesser Egyptian jerboa |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,650,517 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,765,502,549 out of 2,728,222,451 |
Uncovered: 1,368,383 out of 36,555,494 |
| Lesser Egyptian jerboa |
Uncovered: 1,945,994,845 out of 2,835,250,225 |
Uncovered: 988,238 out of 27,596,411 |
Block size distribution
| Size range | All 1,650,517 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 23,361 |
155.2 kb |
|||
| 10 bp - 100 bp | 167,328 |
9.6 Mb |
24,417 |
1.7 Mb |
|
| 100 bp - 1 kb | 1,159,324 |
512.9 Mb |
120,750 |
44.7 Mb |
|
| 1 kb - 10 kb | 299,720 |
502.7 Mb |
28,371 |
62.9 Mb |
|
| 10 kb - 100 kb | 779 |
12.8 Mb |
1,225 |
26.1 Mb |
|
| 100 kb - 1 Mb | 5 |
626.4 kb |
255 |
108.9 Mb |
|
| 1 Mb - 10 Mb | 252 |
704.3 Mb |
|||
| 10 Mb - 100 Mb | 7 |
90.3 Mb |
|||