Zebrafish vs Channel bull blenny LastZ results
Zebrafish (Danio rerio, GRCz11) and Channel bull blenny (Cottoperca gobio, fCotGob3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 98. 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 | Channel bull blenny |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 320,780 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,311,489,612 out of 1,373,471,384 |
Uncovered: 9,661,110 out of 42,031,845 |
| Channel bull blenny |
Uncovered: 547,808,960 out of 609,391,784 |
Uncovered: 7,638,099 out of 37,075,790 |
Block size distribution
| Size range | All 320,780 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,180 |
10.1 kb |
|||
| 10 bp - 100 bp | 50,917 |
3.6 Mb |
17,052 |
1.3 Mb |
|
| 100 bp - 1 kb | 262,223 |
65.0 Mb |
78,221 |
23.8 Mb |
|
| 1 kb - 10 kb | 5,434 |
8.8 Mb |
13,635 |
34.5 Mb |
|
| 10 kb - 100 kb | 26 |
370.4 kb |
773 |
15.5 Mb |
|
| 100 kb - 1 Mb | 18 |
2.8 Mb |
|||