Pig vs Pig USMARC LastZ results
Pig (Sus scrofa, Sscrofa11.1) and Pig USMARC (Sus scrofa, USMARCv1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 97. 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) | 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 | Pig | Pig USMARC |
|---|---|---|
| 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 85,199 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Pig |
Uncovered: 47,444,807 out of 2,501,912,388 |
Uncovered: 207,907 out of 34,917,531 |
| Pig USMARC |
Uncovered: 362,836,069 out of 2,755,438,035 |
Uncovered: 1,340,304 out of 35,166,034 |
Block size distribution
| Size range | All 85,199 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,066 |
13.1 kb |
|||
| 10 bp - 100 bp | 13,386 |
635.3 kb |
3,245 |
190.0 kb |
|
| 100 bp - 1 kb | 22,007 |
8.1 Mb |
8,477 |
2.9 Mb |
|
| 1 kb - 10 kb | 18,286 |
73.9 Mb |
4,016 |
15.0 Mb |
|
| 10 kb - 100 kb | 22,124 |
856.2 Mb |
2,135 |
69.5 Mb |
|
| 100 kb - 1 Mb | 7,321 |
1.5 Gb |
313 |
74.1 Mb |
|
| 1 Mb - 10 Mb | 9 |
10.2 Mb |
26 |
48.7 Mb |
|
| 10 Mb - 100 Mb | 7 |
483.1 Mb |
|||
| 100 Mb - 1 Gb | 12 |
1.8 Gb |
|||