Oryza sativa Japonica Group vs Helianthus annuus LastZ Results
Back to all analyses
Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 229,529
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 341,316,294 out of 375,049,285 |
Uncovered: 14,833,725 out of 34,403,043 |
Helianthus annuus |
Uncovered: 2,974,593,597 out of 3,027,844,945 |
Uncovered: 22,768,609 out of 54,343,734 |
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 Group | Helianthus annuus | |
---|---|---|
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} |