Oryza glaberrima vs Leersia perrieri LastZ Results
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Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glaberrima 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: 211,120
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza glaberrima |
Uncovered: 164,334,368 out of 285,037,524 |
Uncovered: 2,863,400 out of 36,404,702 |
Leersia perrieri |
Uncovered: 165,494,403 out of 266,687,832 |
Uncovered: 8,625,957 out of 36,899,367 |
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 glaberrima | Leersia perrieri | |
---|---|---|
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} |