Zebrafish vs Bicolor damselfish LastZ results
Zebrafish (Danio rerio, GRCz11) and Bicolor damselfish (Stegastes partitus, Stegastes_partitus-1.0.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Zebrafish 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 | Zebrafish | Bicolor damselfish |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 311,530 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,309,002,855 out of 1,373,471,384 |
Uncovered: 9,462,189 out of 42,031,845 |
| Bicolor damselfish |
Uncovered: 739,197,946 out of 800,491,834 |
Uncovered: 6,276,305 out of 36,236,516 |
Block size distribution
| Size range | All 311,530 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,914 |
8.7 kb |
|||
| 10 bp - 100 bp | 46,376 |
3.4 Mb |
14,429 |
1.1 Mb |
|
| 100 bp - 1 kb | 256,785 |
63.1 Mb |
77,681 |
24.0 Mb |
|
| 1 kb - 10 kb | 6,418 |
11.3 Mb |
15,070 |
37.8 Mb |
|
| 10 kb - 100 kb | 37 |
682.8 kb |
748 |
14.5 Mb |
|
| 100 kb - 1 Mb | 9 |
1.1 Mb |
|||