Mouse vs Kangaroo rat LastZ results
Mouse (Mus musculus, GRCm39) and Kangaroo rat (Dipodomys ordii, Dord_2.0) 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 | Kangaroo rat |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,143,749 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 2,028,000,841 out of 2,728,222,451 |
Uncovered: 3,011,947 out of 61,150,575 |
| Kangaroo rat |
Uncovered: 1,590,079,276 out of 2,236,368,823 |
Uncovered: 586,004 out of 26,238,403 |
Block size distribution
| Size range | All 1,143,749 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 9,991 |
67.3 kb |
|||
| 10 bp - 100 bp | 107,362 |
6.4 Mb |
15,066 |
1.1 Mb |
|
| 100 bp - 1 kb | 800,291 |
363.6 Mb |
68,216 |
26.3 Mb |
|
| 1 kb - 10 kb | 225,884 |
383.5 Mb |
24,328 |
60.9 Mb |
|
| 10 kb - 100 kb | 218 |
2.8 Mb |
700 |
16.3 Mb |
|
| 100 kb - 1 Mb | 3 |
409.4 kb |
249 |
104.8 Mb |
|
| 1 Mb - 10 Mb | 182 |
465.6 Mb |
|||
| 10 Mb - 100 Mb | 6 |
81.8 Mb |
|||