Human vs Pig USMARC LastZ results
Human (Homo sapiens, GRCh38) and Pig USMARC (Sus scrofa, USMARCv1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 97. Human 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 |
| 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 | Human | Pig USMARC |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 2,311,298 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,605,457,028 out of 3,099,750,718 |
Uncovered: 1,910,457 out of 38,571,754 |
| Pig USMARC |
Uncovered: 1,357,522,016 out of 2,755,438,035 |
Uncovered: 3,037,098 out of 35,166,034 |
Block size distribution
| Size range | All 2,311,298 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 88,385 |
587.7 kb |
|||
| 10 bp - 100 bp | 285,864 |
13.9 Mb |
17,702 |
1.2 Mb |
|
| 100 bp - 1 kb | 1,428,197 |
635.1 Mb |
60,765 |
21.9 Mb |
|
| 1 kb - 10 kb | 507,993 |
941.8 Mb |
19,633 |
49.6 Mb |
|
| 10 kb - 100 kb | 813 |
12.6 Mb |
2,146 |
59.9 Mb |
|
| 100 kb - 1 Mb | 46 |
5.9 Mb |
324 |
84.3 Mb |
|
| 1 Mb - 10 Mb | 70 |
264.0 Mb |
|||
| 10 Mb - 100 Mb | 42 |
1.1 Gb |
|||