Sheepshead minnow vs Zebrafish LastZ results
Sheepshead minnow (Cyprinodon variegatus, C_variegatus-1.0) and Zebrafish (Danio rerio, GRCz11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Sheepshead minnow 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 | Sheepshead minnow | Zebrafish |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 284,498 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Sheepshead minnow |
Uncovered: 980,080,348 out of 1,035,184,475 |
Uncovered: 7,148,122 out of 35,763,670 |
| Zebrafish |
Uncovered: 1,313,745,221 out of 1,373,471,384 |
Uncovered: 10,314,909 out of 42,031,845 |
Block size distribution
| Size range | All 284,498 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,702 |
7.5 kb |
|||
| 10 bp - 100 bp | 41,305 |
3.0 Mb |
14,571 |
1.1 Mb |
|
| 100 bp - 1 kb | 234,812 |
57.9 Mb |
83,873 |
26.1 Mb |
|
| 1 kb - 10 kb | 6,674 |
12.1 Mb |
15,269 |
36.9 Mb |
|
| 10 kb - 100 kb | 5 |
74.9 kb |
491 |
8.7 Mb |
|
| 100 kb - 1 Mb | 3 |
371.8 kb |
|||