Oryza meridionalis vs Oryza sativa Japonica Group LastZ Results
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Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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: 343,106
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza meridionalis |
Uncovered: 97,874,978 out of 335,668,232 |
Uncovered: 420,569 out of 35,224,824 |
Oryza sativa Japonica Group |
Uncovered: 183,181,862 out of 374,424,240 |
Uncovered: 5,949,666 out of 34,124,807 |
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 meridionalis | Oryza sativa Japonica Group | |
---|---|---|
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} |