Zebrafish vs Siamese fighting fish LastZ results
Zebrafish (Danio rerio, GRCz11) and Siamese fighting fish (Betta splendens, fBetSpl5.2) 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 | Siamese fighting fish |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 269,872 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,319,708,434 out of 1,373,471,384 |
Uncovered: 11,694,595 out of 42,031,845 |
| Siamese fighting fish |
Uncovered: 387,981,915 out of 441,371,523 |
Uncovered: 11,499,621 out of 40,133,352 |
Block size distribution
| Size range | All 269,872 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,837 |
8.3 kb |
|||
| 10 bp - 100 bp | 41,312 |
3.0 Mb |
10,795 |
802.7 kb |
|
| 100 bp - 1 kb | 222,601 |
55.3 Mb |
54,727 |
17.1 Mb |
|
| 1 kb - 10 kb | 4,116 |
6.5 Mb |
11,962 |
31.1 Mb |
|
| 10 kb - 100 kb | 6 |
86.4 kb |
701 |
13.9 Mb |
|
| 100 kb - 1 Mb | 13 |
2.0 Mb |
|||