Japanese medaka HdrR vs Northern pike LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Northern pike (Esox lucius, fEsoLuc1.pri) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 112. Japanese medaka HdrR 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 | Japanese medaka HdrR | Northern pike |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | 10,100,000 |
| Masking options |
Statistics over 269,333 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 665,299,749 out of 734,057,086 |
Uncovered: 9,234,738 out of 40,334,262 |
| Northern pike |
Uncovered: 851,823,544 out of 918,748,614 |
Uncovered: 16,403,397 out of 47,202,559 |
Block size distribution
| Size range | All 269,333 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,492 |
7.7 kb |
|||
| 10 bp - 100 bp | 37,126 |
2.6 Mb |
5,466 |
399.4 kb |
|
| 100 bp - 1 kb | 223,777 |
60.8 Mb |
30,096 |
9.6 Mb |
|
| 1 kb - 10 kb | 6,927 |
10.6 Mb |
7,136 |
19.7 Mb |
|
| 10 kb - 100 kb | 11 |
164.3 kb |
922 |
24.0 Mb |
|
| 100 kb - 1 Mb | 85 |
20.4 Mb |
|||