Pig vs Pig - Chenghua LastZ results
Pig (Sus scrofa, Sscrofa11.1) and Pig - Chenghua (Sus scrofa, ASM3744751v1) 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 - Chenghua |
|---|---|---|
| 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 100,949 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Pig |
Uncovered: 43,999,818 out of 2,501,912,388 |
Uncovered: 278,276 out of 35,448,596 |
| Pig - Chenghua |
Uncovered: 296,371,328 out of 2,714,138,220 |
Uncovered: 497,002 out of 34,227,502 |
Block size distribution
| Size range | All 100,949 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,813 |
19.0 kb |
|||
| 10 bp - 100 bp | 11,833 |
510.5 kb |
2,385 |
143.6 kb |
|
| 100 bp - 1 kb | 18,439 |
7.2 Mb |
7,116 |
2.4 Mb |
|
| 1 kb - 10 kb | 23,687 |
105.3 Mb |
2,603 |
8.8 Mb |
|
| 10 kb - 100 kb | 38,374 |
1.4 Gb |
889 |
30.6 Mb |
|
| 100 kb - 1 Mb | 5,802 |
954.1 Mb |
137 |
33.5 Mb |
|
| 1 Mb - 10 Mb | 1 |
1.1 Mb |
14 |
35.9 Mb |
|
| 10 Mb - 100 Mb | 8 |
425.5 Mb |
|||
| 100 Mb - 1 Gb | 13 |
1.9 Gb |
|||