Orange clownfish vs Zebrafish LastZ results
Orange clownfish (Amphiprion percula, Nemo_v1) and Zebrafish (Danio rerio, GRCz11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Orange clownfish 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 | Orange clownfish | Zebrafish |
|---|---|---|
| Chunk size | 10,000,000 | 10,000,000 |
| Overlap | 0 | 0 |
| Group set size | 0 | 0 |
| Masking options |
Statistics over 312,363 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Orange clownfish |
Uncovered: 847,968,262 out of 908,939,294 |
Uncovered: 7,311,824 out of 38,226,868 |
| Zebrafish |
Uncovered: 1,312,527,915 out of 1,373,471,384 |
Uncovered: 9,707,915 out of 42,031,845 |
Block size distribution
| Size range | All 312,363 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,963 |
9.0 kb |
|||
| 10 bp - 100 bp | 46,768 |
3.4 Mb |
14,685 |
1.1 Mb |
|
| 100 bp - 1 kb | 258,529 |
63.5 Mb |
78,308 |
24.0 Mb |
|
| 1 kb - 10 kb | 5,100 |
8.1 Mb |
13,959 |
34.4 Mb |
|
| 10 kb - 100 kb | 3 |
40.1 kb |
664 |
13.4 Mb |
|
| 100 kb - 1 Mb | 15 |
2.2 Mb |
|||