Japanese medaka HdrR vs Climbing perch LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Climbing perch (Anabas testudineus, fAnaTes1.3) 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 | Climbing perch |
|---|---|---|
| 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 332,300 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 580,668,960 out of 734,057,086 |
Uncovered: 6,591,432 out of 40,334,262 |
| Climbing perch |
Uncovered: 394,525,966 out of 555,641,398 |
Uncovered: 8,542,734 out of 42,904,056 |
Block size distribution
| Size range | All 332,300 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,216 |
7.6 kb |
|||
| 10 bp - 100 bp | 24,725 |
1.6 Mb |
1,778 |
129.7 kb |
|
| 100 bp - 1 kb | 266,073 |
104.1 Mb |
9,438 |
3.1 Mb |
|
| 1 kb - 10 kb | 40,265 |
65.1 Mb |
2,076 |
5.5 Mb |
|
| 10 kb - 100 kb | 21 |
287.4 kb |
399 |
12.6 Mb |
|
| 100 kb - 1 Mb | 127 |
36.9 Mb |
|||
| 1 Mb - 10 Mb | 36 |
112.8 Mb |
|||