Pig vs Pig - Berkshire LastZ results
Pig (Sus scrofa, Sscrofa11.1) and Pig - Berkshire (Sus scrofa, Berkshire_pig_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 98. 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) | Primate:
A C G T
90 -330 -236 -356
-330 100 -318 -236
-236 -318 100 -330
-356 -236 -330 90
|
Chunking parameters
| Parameter | Pig | Pig - Berkshire |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 139,816 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Pig |
Uncovered: 92,350,770 out of 2,501,912,388 |
Uncovered: 1,187,897 out of 35,828,571 |
| Pig - Berkshire |
Uncovered: 71,200,638 out of 2,434,706,773 |
Uncovered: 305,656 out of 34,511,197 |
Block size distribution
| Size range | All 139,816 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,335 |
7.2 kb |
|||
| 10 bp - 100 bp | 10,048 |
527.5 kb |
4,846 |
273.1 kb |
|
| 100 bp - 1 kb | 38,330 |
15.4 Mb |
21,758 |
8.0 Mb |
|
| 1 kb - 10 kb | 38,399 |
161.7 Mb |
5,882 |
18.0 Mb |
|
| 10 kb - 100 kb | 47,523 |
1.6 Gb |
2,016 |
67.1 Mb |
|
| 100 kb - 1 Mb | 4,181 |
611.6 Mb |
1,574 |
664.5 Mb |
|
| 1 Mb - 10 Mb | 769 |
1.7 Gb |
|||