Cat vs Leopard LastZ results
Cat (Felis catus, Felis_catus_9.0) and Leopard (Panthera pardus, PanPar1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 93. Cat 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 | Cat | Leopard |
|---|---|---|
| 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 652,238 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Cat |
Uncovered: 158,453,569 out of 2,521,863,845 |
Uncovered: 67,861 out of 31,563,304 |
| Leopard |
Uncovered: 257,472,510 out of 2,578,019,207 |
Uncovered: 879,525 out of 30,973,212 |
Block size distribution
| Size range | All 652,238 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 7,095 |
43.7 kb |
|||
| 10 bp - 100 bp | 44,019 |
2.2 Mb |
14,033 |
847.0 kb |
|
| 100 bp - 1 kb | 171,752 |
74.7 Mb |
52,689 |
16.5 Mb |
|
| 1 kb - 10 kb | 374,239 |
1.5 Gb |
5,835 |
14.0 Mb |
|
| 10 kb - 100 kb | 55,105 |
824.5 Mb |
811 |
26.7 Mb |
|
| 100 kb - 1 Mb | 28 |
3.7 Mb |
159 |
59.3 Mb |
|
| 1 Mb - 10 Mb | 129 |
499.8 Mb |
|||
| 10 Mb - 100 Mb | 77 |
1.8 Gb |
|||