Mouse vs Guinea Pig LastZ results
Mouse (Mus musculus, GRCm39) and Guinea Pig (Cavia porcellus, Cavpor3.0) 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 | Guinea Pig |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,215,000 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,927,562,063 out of 2,728,222,451 |
Uncovered: 3,380,762 out of 72,028,242 |
| Guinea Pig |
Uncovered: 1,957,119,480 out of 2,723,219,641 |
Uncovered: 2,448,168 out of 59,632,306 |
Block size distribution
| Size range | All 1,215,000 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 11,664 |
77.1 kb |
|||
| 10 bp - 100 bp | 109,252 |
6.3 Mb |
15,689 |
1.1 Mb |
|
| 100 bp - 1 kb | 813,057 |
374.4 Mb |
61,852 |
23.1 Mb |
|
| 1 kb - 10 kb | 280,799 |
483.9 Mb |
17,449 |
39.5 Mb |
|
| 10 kb - 100 kb | 227 |
3.3 Mb |
729 |
18.7 Mb |
|
| 100 kb - 1 Mb | 1 |
139.7 kb |
278 |
113.2 Mb |
|
| 1 Mb - 10 Mb | 202 |
593.3 Mb |
|||
| 10 Mb - 100 Mb | 6 |
79.2 Mb |
|||