Mouse vs Arctic ground squirrel LastZ results
Mouse (Mus musculus, GRCm39) and Arctic ground squirrel (Urocitellus parryii, ASM342692v1) 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 | Arctic ground squirrel |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,432,388 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,751,476,934 out of 2,728,222,451 |
Uncovered: 1,577,790 out of 36,555,494 |
| Arctic ground squirrel |
Uncovered: 1,578,321,422 out of 2,520,505,282 |
Uncovered: 1,424,969 out of 31,635,636 |
Block size distribution
| Size range | All 1,432,388 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 20,603 |
138.2 kb |
|||
| 10 bp - 100 bp | 130,280 |
7.0 Mb |
9,737 |
682.8 kb |
|
| 100 bp - 1 kb | 937,450 |
439.0 Mb |
52,961 |
22.0 Mb |
|
| 1 kb - 10 kb | 343,158 |
608.4 Mb |
20,976 |
54.6 Mb |
|
| 10 kb - 100 kb | 894 |
11.5 Mb |
1,662 |
36.9 Mb |
|
| 100 kb - 1 Mb | 3 |
397.8 kb |
611 |
246.9 Mb |
|
| 1 Mb - 10 Mb | 320 |
705.4 Mb |
|||