Pig vs Pig - Norwegian Landrace LastZ results
Pig (Sus scrofa, Sscrofa11.1) and Pig - Norwegian Landrace (Sus scrofa, norwegian_landrace) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 116. 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 - Norwegian Landrace |
|---|---|---|
| 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 60,176 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Pig |
Uncovered: 47,376,976 out of 2,501,912,388 |
Uncovered: 285,357 out of 35,448,596 |
| Pig - Norwegian Landrace |
Uncovered: 208,012,768 out of 2,633,804,232 |
Uncovered: 528,677 out of 33,938,251 |
Block size distribution
| Size range | All 60,176 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,573 |
10.7 kb |
|||
| 10 bp - 100 bp | 6,782 |
289.9 kb |
1,252 |
74.8 kb |
|
| 100 bp - 1 kb | 10,235 |
4.0 Mb |
3,859 |
1.4 Mb |
|
| 1 kb - 10 kb | 13,099 |
57.5 Mb |
1,436 |
4.7 Mb |
|
| 10 kb - 100 kb | 21,310 |
826.3 Mb |
747 |
26.3 Mb |
|
| 100 kb - 1 Mb | 7,169 |
1.6 Gb |
134 |
31.8 Mb |
|
| 1 Mb - 10 Mb | 8 |
9.9 Mb |
10 |
25.7 Mb |
|
| 10 Mb - 100 Mb | 6 |
406.0 Mb |
|||
| 100 Mb - 1 Gb | 13 |
2.0 Gb |
|||