Japanese medaka HdrR vs Zig-zag eel LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Zig-zag eel (Mastacembelus armatus, fMasArm1.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 103. 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 | Zig-zag eel |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 369,636 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 576,221,427 out of 734,057,086 |
Uncovered: 6,017,127 out of 40,334,262 |
| Zig-zag eel |
Uncovered: 423,355,157 out of 591,951,587 |
Uncovered: 4,742,815 out of 39,800,582 |
Block size distribution
| Size range | All 369,636 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,708 |
10.4 kb |
|||
| 10 bp - 100 bp | 33,045 |
2.1 Mb |
3,584 |
258.1 kb |
|
| 100 bp - 1 kb | 293,634 |
111.4 Mb |
16,717 |
5.6 Mb |
|
| 1 kb - 10 kb | 41,233 |
66.8 Mb |
3,759 |
9.2 Mb |
|
| 10 kb - 100 kb | 16 |
217.4 kb |
443 |
13.4 Mb |
|
| 100 kb - 1 Mb | 136 |
42.5 Mb |
|||
| 1 Mb - 10 Mb | 35 |
109.5 Mb |
|||