Mouse vs Shrew mouse LastZ results
Mouse (Mus musculus, GRCm39) and Shrew mouse (Mus pahari, PAHARI_EIJ_v1.1) 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 |
| 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 | Shrew mouse |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options |
Statistics over 1,371,457 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 544,613,087 out of 2,728,222,451 |
Uncovered: 248,010 out of 39,092,596 |
| Shrew mouse |
Uncovered: 465,125,493 out of 2,475,012,951 |
Uncovered: 94,509 out of 32,578,444 |
Block size distribution
| Size range | All 1,371,457 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 22,636 |
138.7 kb |
|||
| 10 bp - 100 bp | 140,856 |
7.7 Mb |
36,142 |
2.3 Mb |
|
| 100 bp - 1 kb | 578,700 |
260.2 Mb |
103,180 |
35.1 Mb |
|
| 1 kb - 10 kb | 615,830 |
1.8 Gb |
30,398 |
83.4 Mb |
|
| 10 kb - 100 kb | 13,280 |
189.5 Mb |
3,477 |
73.8 Mb |
|
| 100 kb - 1 Mb | 155 |
20.0 Mb |
224 |
29.9 Mb |
|
| 1 Mb - 10 Mb | 6 |
35.2 Mb |
|||
| 10 Mb - 100 Mb | 26 |
1.4 Gb |
|||
| 100 Mb - 1 Gb | 5 |
619.6 Mb |
|||