C.savignyi vs Zebrafish LastZ results
C.savignyi (Ciona savignyi, CSAV2.0) and Zebrafish (Danio rerio, GRCz11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 92. C.savignyi 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) | |
| 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 | C.savignyi | Zebrafish |
|---|---|---|
| Chunk size | 10,000,000 | 10,000,000 |
| Overlap | 0 | 0 |
| Group set size | 0 | 0 |
| Masking options |
Statistics over 65,331 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| C.savignyi |
Uncovered: 171,307,240 out of 177,003,750 |
Uncovered: 10,121,028 out of 13,817,826 |
| Zebrafish |
Uncovered: 1,365,154,150 out of 1,373,471,384 |
Uncovered: 35,473,000 out of 42,031,845 |
Block size distribution
| Size range | All 65,331 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 255 |
1.2 kb |
|||
| 10 bp - 100 bp | 19,361 |
1.5 Mb |
7,688 |
581.7 kb |
|
| 100 bp - 1 kb | 45,498 |
8.0 Mb |
25,108 |
6.4 Mb |
|
| 1 kb - 10 kb | 217 |
328.3 kb |
1,311 |
2.4 Mb |
|
| 10 kb - 100 kb | 17 |
337.7 kb |
|||