Zebrafish vs Coho salmon LastZ results
Zebrafish (Danio rerio, GRCz11) and Coho salmon (Oncorhynchus kisutch, Okis_V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 101. 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 | Coho salmon |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 316,478 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,300,053,355 out of 1,373,471,384 |
Uncovered: 7,152,209 out of 42,031,845 |
| Coho salmon |
Uncovered: 2,308,457,869 out of 2,375,894,934 |
Uncovered: 51,066,105 out of 81,688,917 |
Block size distribution
| Size range | All 316,478 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,987 |
13.4 kb |
|||
| 10 bp - 100 bp | 47,833 |
3.3 Mb |
13,618 |
1.0 Mb |
|
| 100 bp - 1 kb | 259,849 |
66.0 Mb |
77,290 |
24.2 Mb |
|
| 1 kb - 10 kb | 5,802 |
9.3 Mb |
13,286 |
33.8 Mb |
|
| 10 kb - 100 kb | 7 |
96.8 kb |
815 |
16.4 Mb |
|
| 100 kb - 1 Mb | 20 |
3.4 Mb |
|||