Oryza sativa Japonica Group vs Ostreococcus lucimarinus LastZ results
Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901, ASM9206v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
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 |
Chunking parameters
Parameter | Oryza sativa Japonica Group | Ostreococcus lucimarinus |
---|---|---|
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} |
Statistics over 12,496 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 372,518,183 out of 375,049,285 |
Uncovered: 32,311,523 out of 34,403,043 |
Ostreococcus lucimarinus |
Uncovered: 11,712,469 out of 13,204,888 |
Uncovered: 7,840,072 out of 9,226,744 |
Block size distribution
Size range | All 12,496 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 49 |
296.0 bp |
|||
10 bp - 100 bp | 3,432 |
253.2 kb |
574 |
41.1 kb |
|
100 bp - 1 kb | 8,705 |
2.1 Mb |
3,637 |
1.5 Mb |
|
1 kb - 10 kb | 310 |
448.5 kb |
809 |
1.3 Mb |