Oryza sativa Japonica vs Oryza rufipogon LastZ Results
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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza sativa Japonica was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.
Results
Number of alignment blocks: 103,093
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 70,757,579 out of 373,245,519 |
Uncovered: 337,005 out of 44,520,596 |
Oryza rufipogon |
Uncovered: 51,237,990 out of 338,040,714 |
Uncovered: 1,152,224 out of 42,764,129 |
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 |
Other parameters (other) | --ambiguous=iupac |
Chunking parameters
Oryza sativa Japonica | Oryza rufipogon | |
---|---|---|
Chunk size | 30,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} |