Japanese medaka HdrR vs Monterrey platyfish LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Monterrey platyfish (Xiphophorus couchianus, Xiphophorus_couchianus-4.0.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. 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 | Monterrey platyfish |
|---|---|---|
| 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 313,691 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 591,027,515 out of 734,057,086 |
Uncovered: 7,820,707 out of 40,334,262 |
| Monterrey platyfish |
Uncovered: 569,617,491 out of 708,396,389 |
Uncovered: 3,562,049 out of 27,552,751 |
Block size distribution
| Size range | All 313,691 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 986 |
5.4 kb |
|||
| 10 bp - 100 bp | 23,694 |
1.6 Mb |
3,537 |
258.3 kb |
|
| 100 bp - 1 kb | 257,866 |
98.0 Mb |
20,089 |
7.1 Mb |
|
| 1 kb - 10 kb | 30,932 |
49.2 Mb |
6,558 |
18.4 Mb |
|
| 10 kb - 100 kb | 213 |
5.2 Mb |
957 |
26.0 Mb |
|
| 100 kb - 1 Mb | 175 |
50.1 Mb |
|||
| 1 Mb - 10 Mb | 19 |
52.2 Mb |
|||