Japanese medaka HdrR vs Coho salmon LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Coho salmon (Oncorhynchus kisutch, Okis_V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 101. 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 | Coho salmon |
|---|---|---|
| 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 579,998 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 654,374,799 out of 734,057,086 |
Uncovered: 8,239,217 out of 40,334,262 |
| Coho salmon |
Uncovered: 2,237,856,149 out of 2,375,894,934 |
Uncovered: 24,462,346 out of 81,688,917 |
Block size distribution
| Size range | All 579,998 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 6,247 |
28.9 kb |
|||
| 10 bp - 100 bp | 92,447 |
6.3 Mb |
16,427 |
1.2 Mb |
|
| 100 bp - 1 kb | 467,883 |
124.3 Mb |
86,363 |
27.6 Mb |
|
| 1 kb - 10 kb | 13,411 |
20.4 Mb |
18,684 |
48.2 Mb |
|
| 10 kb - 100 kb | 10 |
144.1 kb |
1,562 |
38.1 Mb |
|
| 100 kb - 1 Mb | 144 |
35.9 Mb |
|||