Mouse vs Chinese hamster PICR LastZ results
Mouse (Mus musculus, GRCm39) and Chinese hamster PICR (Cricetulus griseus, CriGri-PICRH-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 115. 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 | Chinese hamster PICR |
|---|---|---|
| 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 1,974,373 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,102,520,163 out of 2,728,222,451 |
Uncovered: 658,982 out of 39,092,596 |
| Chinese hamster PICR |
Uncovered: 847,448,483 out of 2,366,634,374 |
Uncovered: 2,939,662 out of 37,747,936 |
Block size distribution
| Size range | All 1,974,373 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 52,744 |
340.0 kb |
|||
| 10 bp - 100 bp | 203,624 |
10.5 Mb |
25,878 |
1.8 Mb |
|
| 100 bp - 1 kb | 1,136,486 |
510.6 Mb |
88,100 |
30.4 Mb |
|
| 1 kb - 10 kb | 580,462 |
1.2 Gb |
22,797 |
58.8 Mb |
|
| 10 kb - 100 kb | 1,048 |
13.7 Mb |
1,901 |
42.5 Mb |
|
| 100 kb - 1 Mb | 9 |
1.2 Mb |
69 |
21.5 Mb |
|
| 1 Mb - 10 Mb | 51 |
212.2 Mb |
|||
| 10 Mb - 100 Mb | 36 |
1.4 Gb |
|||