Pig vs Pig - euw1 (european wild boar) LastZ results
Pig (Sus scrofa, Sscrofa11.1) and Pig - euw1 (european wild boar) (Sus scrofa, ASM2165605v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 113. Pig 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) | 5000 |
| Threshold for gapped extension (L) | 5000 |
| Threshold for alignments between gapped alignment blocks (H) | 3000 |
| Masking count (M) | 10 |
| 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 | Pig | Pig - euw1 (european wild boar) |
|---|---|---|
| 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 118,179 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Pig |
Uncovered: 49,305,341 out of 2,501,912,388 |
Uncovered: 329,736 out of 35,448,596 |
| Pig - euw1 (european wild boar) |
Uncovered: 65,773,527 out of 2,457,990,317 |
Uncovered: 541,806 out of 32,847,998 |
Block size distribution
| Size range | All 118,179 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,507 |
16.2 kb |
|||
| 10 bp - 100 bp | 14,425 |
692.5 kb |
3,624 |
221.4 kb |
|
| 100 bp - 1 kb | 31,307 |
12.4 Mb |
11,974 |
4.5 Mb |
|
| 1 kb - 10 kb | 28,766 |
111.1 Mb |
9,411 |
31.4 Mb |
|
| 10 kb - 100 kb | 34,994 |
1.3 Gb |
1,978 |
48.8 Mb |
|
| 100 kb - 1 Mb | 6,180 |
1.0 Gb |
132 |
41.6 Mb |
|
| 1 Mb - 10 Mb | 89 |
352.0 Mb |
|||
| 10 Mb - 100 Mb | 70 |
2.0 Gb |
|||