Oryza longistaminata vs Oryza nivara LastZ Results
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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza longistaminata 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: 256,996
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza longistaminata |
Uncovered: 89,441,394 out of 326,442,508 |
Uncovered: 904,271 out of 34,512,301 |
Oryza sativa f. spontanea |
Uncovered: 128,808,237 out of 337,950,324 |
Uncovered: 7,456,510 out of 42,562,444 |
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 longistaminata | Oryza nivara | |
---|---|---|
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} |