Oryza sativa Japonica vs Chlamydomonas reinhardtii LastZ Results
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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 17,708
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 371,894,138 out of 374,424,240 |
Uncovered: 32,142,092 out of 34,124,807 |
Chlamydomonas reinhardtii |
Uncovered: 119,091,354 out of 120,404,952 |
Uncovered: 18,626,415 out of 19,668,972 |
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) |