Zebrafish vs Chinese medaka LastZ results
Zebrafish (Danio rerio, GRCz11) and Chinese medaka (Oryzias sinensis, ASM858656v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 100. 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 | Chinese medaka |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 296,776 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,296,545,735 out of 1,373,471,384 |
Uncovered: 9,941,821 out of 42,031,845 |
| Chinese medaka |
Uncovered: 755,666,961 out of 813,986,518 |
Uncovered: 8,105,893 out of 33,987,082 |
Block size distribution
| Size range | All 296,776 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,931 |
8.8 kb |
|||
| 10 bp - 100 bp | 46,399 |
3.4 Mb |
16,155 |
1.2 Mb |
|
| 100 bp - 1 kb | 241,296 |
59.3 Mb |
83,670 |
26.3 Mb |
|
| 1 kb - 10 kb | 6,312 |
12.3 Mb |
15,549 |
37.0 Mb |
|
| 10 kb - 100 kb | 836 |
18.8 Mb |
1,254 |
28.7 Mb |
|
| 100 kb - 1 Mb | 2 |
273.4 kb |
7 |
896.6 kb |
|