Mouse vs Prairie vole LastZ results
Mouse (Mus musculus, GRCm39) and Prairie vole (Microtus ochrogaster, MicOch1.0) 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 | Prairie vole |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 2,086,783 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
Uncovered: 1,065,156,430 out of 2,728,222,451 |
Uncovered: 427,201 out of 36,014,121 |
| Prairie vole |
Uncovered: 797,431,664 out of 2,287,357,235 |
Uncovered: 562,100 out of 30,375,214 |
Block size distribution
| Size range | All 2,086,783 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 51,866 |
331.9 kb |
|||
| 10 bp - 100 bp | 226,531 |
12.0 Mb |
34,756 |
2.4 Mb |
|
| 100 bp - 1 kb | 1,231,431 |
544.0 Mb |
136,905 |
48.5 Mb |
|
| 1 kb - 10 kb | 574,693 |
1.2 Gb |
36,006 |
95.3 Mb |
|
| 10 kb - 100 kb | 2,252 |
33.5 Mb |
3,812 |
73.0 Mb |
|
| 100 kb - 1 Mb | 10 |
1.3 Mb |
150 |
61.4 Mb |
|
| 1 Mb - 10 Mb | 157 |
527.8 Mb |
|||
| 10 Mb - 100 Mb | 46 |
945.2 Mb |
|||