Mouse vs Naked mole-rat female LastZ results
Mouse (Mus musculus, GRCm39) and Naked mole-rat female (Heterocephalus glaber, Naked_mole-rat_maternal) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 110. 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 | Naked mole-rat female |
|---|---|---|
| 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 1,383,900 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,826,141,797 out of 2,728,222,451 |
Uncovered: 1,934,763 out of 36,801,392 |
| Naked mole-rat female |
Uncovered: 1,619,465,578 out of 2,500,150,894 |
Uncovered: 4,026,450 out of 34,454,808 |
Block size distribution
| Size range | All 1,383,900 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 17,234 |
115.1 kb |
|||
| 10 bp - 100 bp | 123,074 |
6.8 Mb |
12,589 |
879.0 kb |
|
| 100 bp - 1 kb | 925,738 |
428.4 Mb |
57,781 |
22.1 Mb |
|
| 1 kb - 10 kb | 317,679 |
545.4 Mb |
15,558 |
33.9 Mb |
|
| 10 kb - 100 kb | 173 |
2.3 Mb |
682 |
18.0 Mb |
|
| 100 kb - 1 Mb | 2 |
279.2 kb |
268 |
100.0 Mb |
|
| 1 Mb - 10 Mb | 176 |
533.5 Mb |
|||
| 10 Mb - 100 Mb | 18 |
275.1 Mb |
|||