Oryza sativa Japonica vs Dioscorea rotundata LastZ Results
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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Dioscorea rotundata (Dioscorea rotundata, TDr96_F1_Pseudo_Chromosome_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 143,155
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 336,707,692 out of 375,049,285 |
Uncovered: 12,491,574 out of 34,403,043 |
Dioscorea rotundata |
Uncovered: 420,726,517 out of 456,674,974 |
Uncovered: 7,368,413 out of 24,441,241 |
Configuration parameters
Parameter | Value |
---|---|
Gap open penalty (O) | 400 |
Gap extend penalty (E) | 30 |
HSP threshold (K) | |
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 | Dioscorea rotundata | |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |