Zebrafish vs Hagfish LastZ results
Zebrafish (Danio rerio, GRCz11) and Hagfish (Eptatretus burgeri, Eburgeri_3.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 93. 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 | Hagfish |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 131,497 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,351,325,746 out of 1,373,471,384 |
Uncovered: 26,999,293 out of 42,031,845 |
| Hagfish |
Uncovered: 2,591,215,211 out of 2,608,383,542 |
Uncovered: 14,263,561 out of 23,977,300 |
Block size distribution
| Size range | All 131,497 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 587 |
2.5 kb |
|||
| 10 bp - 100 bp | 23,761 |
1.8 Mb |
13,428 |
1.0 Mb |
|
| 100 bp - 1 kb | 105,443 |
21.0 Mb |
73,312 |
18.6 Mb |
|
| 1 kb - 10 kb | 1,641 |
4.4 Mb |
3,000 |
6.8 Mb |
|
| 10 kb - 100 kb | 65 |
786.8 kb |
108 |
1.5 Mb |
|