Vitis vinifera vs Setaria italica LastZ Results
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Vitis vinifera (Vitis vinifera, 12X) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 174,610
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Vitis vinifera |
Uncovered: 446,871,815 out of 486,265,422 |
Uncovered: 10,052,844 out of 32,794,161 |
Setaria italica |
Uncovered: 369,279,846 out of 405,732,883 |
Uncovered: 15,594,245 out of 39,583,990 |
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
Vitis vinifera | Setaria italica | |
---|---|---|
Chunk size | 50,000,000 | 100,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 100,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |