Human vs Javanese ricefish LastZ results
Human (Homo sapiens, GRCh38) and Javanese ricefish (Oryzias javanicus, OJAV_1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 100. Human 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 | Human | Javanese ricefish |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 254,871 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,063,862,690 out of 3,096,649,726 |
Uncovered: 15,254,015 out of 35,610,692 |
| Javanese ricefish |
Uncovered: 778,062,643 out of 809,679,899 |
Uncovered: 14,507,343 out of 34,799,773 |
Block size distribution
| Size range | All 254,871 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,543 |
7.0 kb |
|||
| 10 bp - 100 bp | 51,675 |
3.9 Mb |
15,703 |
1.2 Mb |
|
| 100 bp - 1 kb | 200,039 |
40.2 Mb |
84,285 |
25.4 Mb |
|
| 1 kb - 10 kb | 1,607 |
2.5 Mb |
9,780 |
18.9 Mb |
|
| 10 kb - 100 kb | 6 |
147.2 kb |
69 |
1.1 Mb |
|
| 100 kb - 1 Mb | 1 |
139.1 kb |
2 |
247.1 kb |
|