Japanese medaka HdrR vs Atlantic cod LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Atlantic cod (Gadus morhua, gadMor3.0) 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 | Atlantic cod |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 325,259 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 663,380,176 out of 734,057,086 |
Uncovered: 9,160,178 out of 40,334,262 |
| Atlantic cod |
Uncovered: 592,043,782 out of 669,949,713 |
Uncovered: 10,913,054 out of 43,237,926 |
Block size distribution
| Size range | All 325,259 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,062 |
10.3 kb |
|||
| 10 bp - 100 bp | 48,360 |
3.4 Mb |
8,066 |
587.6 kb |
|
| 100 bp - 1 kb | 266,958 |
68.9 Mb |
37,534 |
11.9 Mb |
|
| 1 kb - 10 kb | 7,836 |
12.7 Mb |
8,322 |
21.1 Mb |
|
| 10 kb - 100 kb | 39 |
1.3 Mb |
841 |
23.0 Mb |
|
| 100 kb - 1 Mb | 4 |
471.7 kb |
115 |
26.6 Mb |
|
| 1 Mb - 10 Mb | 3 |
3.6 Mb |
|||