Japanese medaka HdrR vs Stickleback LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Stickleback (Gasterosteus aculeatus aculeatus, GAculeatus_UGA_version5) 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 | Stickleback |
|---|---|---|
| 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 316,065 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 602,441,027 out of 734,057,086 |
Uncovered: 6,715,200 out of 40,334,262 |
| Stickleback |
Uncovered: 338,807,663 out of 471,877,818 |
Uncovered: 8,304,690 out of 41,794,194 |
Block size distribution
| Size range | All 316,065 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,170 |
6.9 kb |
|||
| 10 bp - 100 bp | 27,630 |
1.8 Mb |
2,275 |
165.1 kb |
|
| 100 bp - 1 kb | 257,298 |
94.4 Mb |
11,115 |
3.8 Mb |
|
| 1 kb - 10 kb | 29,942 |
47.7 Mb |
2,843 |
7.6 Mb |
|
| 10 kb - 100 kb | 25 |
362.2 kb |
514 |
15.3 Mb |
|
| 100 kb - 1 Mb | 147 |
39.7 Mb |
|||
| 1 Mb - 10 Mb | 33 |
77.7 Mb |
|||