Zebrafish vs Large yellow croaker LastZ results
Zebrafish (Danio rerio, GRCz11) and Large yellow croaker (Larimichthys crocea, L_crocea_2.0) 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 | Large yellow croaker |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 300,961 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,313,293,545 out of 1,373,471,384 |
Uncovered: 10,292,410 out of 42,031,845 |
| Large yellow croaker |
Uncovered: 597,475,528 out of 657,939,657 |
Uncovered: 10,449,456 out of 42,080,541 |
Block size distribution
| Size range | All 300,961 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,940 |
8.7 kb |
|||
| 10 bp - 100 bp | 44,561 |
3.2 Mb |
12,851 |
953.9 kb |
|
| 100 bp - 1 kb | 249,541 |
62.4 Mb |
68,283 |
21.2 Mb |
|
| 1 kb - 10 kb | 4,913 |
7.7 Mb |
13,196 |
33.7 Mb |
|
| 10 kb - 100 kb | 6 |
81.8 kb |
741 |
15.2 Mb |
|
| 100 kb - 1 Mb | 16 |
2.5 Mb |
|||