Oryza sativa Japonica Group vs Selaginella moellendorffii LastZ Results
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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Selaginella moellendorffii (Selaginella moellendorffii, v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica Group 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: 62,566
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 354,281,791 out of 374,424,240 |
Uncovered: 20,406,463 out of 34,124,807 |
Selaginella moellendorffii |
Uncovered: 200,615,953 out of 212,645,483 |
Uncovered: 32,232,322 out of 41,155,148 |
Configuration parameters
Parameter | Value |
---|---|
Gap open penalty (O) | |
Gap extend penalty (E) | |
HSP threshold (K) | |
Threshold for gapped extension (L) | |
Threshold for alignments between gapped alignment blocks (H) | |
Masking count (M) | |
Seed and Transition value (T) | |
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) |