Japanese medaka HdrR vs Indian medaka LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Indian medaka (Oryzias melastigma, Om_v0.7.RACA) 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 | Indian medaka |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 522,170 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 317,764,289 out of 734,057,086 |
Uncovered: 3,775,995 out of 40,334,262 |
| Indian medaka |
Uncovered: 385,973,684 out of 779,452,910 |
Uncovered: 3,226,165 out of 37,626,793 |
Block size distribution
| Size range | All 522,170 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 6,745 |
44.5 kb |
|||
| 10 bp - 100 bp | 51,815 |
2.9 Mb |
6,192 |
424.7 kb |
|
| 100 bp - 1 kb | 303,450 |
139.7 Mb |
21,341 |
7.5 Mb |
|
| 1 kb - 10 kb | 159,865 |
294.2 Mb |
6,098 |
16.0 Mb |
|
| 10 kb - 100 kb | 295 |
3.8 Mb |
427 |
14.6 Mb |
|
| 100 kb - 1 Mb | 133 |
29.7 Mb |
|||
| 1 Mb - 10 Mb | 22 |
82.2 Mb |
|||
| 10 Mb - 100 Mb | 20 |
290.2 Mb |
|||