Zebrafish vs Japanese medaka HdrR LastZ results
Zebrafish (Danio rerio, GRCz11) and Japanese medaka HdrR (Oryzias latipes, ASM223467v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. 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 | Japanese medaka HdrR |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 226,829 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,321,499,383 out of 1,373,471,384 |
Uncovered: 11,434,927 out of 42,031,845 |
| Japanese medaka HdrR |
Uncovered: 690,054,544 out of 734,057,086 |
Uncovered: 15,187,614 out of 40,334,262 |
Block size distribution
| Size range | All 226,829 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,085 |
4.9 kb |
|||
| 10 bp - 100 bp | 33,347 |
2.5 Mb |
10,275 |
764.9 kb |
|
| 100 bp - 1 kb | 188,781 |
46.2 Mb |
54,221 |
16.6 Mb |
|
| 1 kb - 10 kb | 3,609 |
5.6 Mb |
10,498 |
26.4 Mb |
|
| 10 kb - 100 kb | 6 |
84.4 kb |
525 |
9.9 Mb |
|
| 100 kb - 1 Mb | 1 |
136.2 kb |
7 |
916.9 kb |
|