Zebrafish vs Nile tilapia LastZ results
Zebrafish (Danio rerio, GRCz11) and Nile tilapia (Oreochromis niloticus, O_niloticus_UMD_NMBU) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 99. 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 | Nile tilapia |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 312,698 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,312,879,891 out of 1,373,471,384 |
Uncovered: 9,286,224 out of 42,031,845 |
| Nile tilapia |
Uncovered: 943,156,720 out of 1,005,681,550 |
Uncovered: 18,764,341 out of 51,713,280 |
Block size distribution
| Size range | All 312,698 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,027 |
9.2 kb |
|||
| 10 bp - 100 bp | 47,027 |
3.4 Mb |
14,488 |
1.1 Mb |
|
| 100 bp - 1 kb | 257,796 |
64.3 Mb |
75,893 |
23.8 Mb |
|
| 1 kb - 10 kb | 5,842 |
9.4 Mb |
14,823 |
36.4 Mb |
|
| 10 kb - 100 kb | 6 |
78.9 kb |
695 |
13.7 Mb |
|
| 100 kb - 1 Mb | 15 |
2.2 Mb |
|||