Zebrafish vs Ballan wrasse LastZ results
Zebrafish (Danio rerio, GRCz11) and Ballan wrasse (Labrus bergylta, BallGen_V1) 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 | Ballan wrasse |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 318,125 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,313,956,571 out of 1,373,471,384 |
Uncovered: 9,951,090 out of 42,031,845 |
| Ballan wrasse |
Uncovered: 743,694,985 out of 805,480,521 |
Uncovered: 9,592,343 out of 40,487,195 |
Block size distribution
| Size range | All 318,125 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,014 |
9.1 kb |
|||
| 10 bp - 100 bp | 47,165 |
3.4 Mb |
13,958 |
1.0 Mb |
|
| 100 bp - 1 kb | 263,825 |
64.8 Mb |
76,414 |
23.7 Mb |
|
| 1 kb - 10 kb | 5,113 |
7.9 Mb |
14,783 |
36.3 Mb |
|
| 10 kb - 100 kb | 8 |
105.2 kb |
686 |
13.3 Mb |
|
| 100 kb - 1 Mb | 12 |
2.0 Mb |
|||