Oryza sativa Japonica Group vs Prunus avium LastZ results
Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Prunus avium (Prunus avium, PAV_r1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 | Prunus avium |
---|---|---|
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 140,371 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 341,410,849 out of 375,049,285 |
Uncovered: 13,869,338 out of 34,424,450 |
Prunus avium |
Uncovered: 239,476,712 out of 272,361,615 |
Uncovered: 20,298,956 out of 38,693,511 |
Block size distribution
Size range | All 140,371 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,043 |
5.1 kb |
|||
10 bp - 100 bp | 22,167 |
1.5 Mb |
4,851 |
349.4 kb |
|
100 bp - 1 kb | 109,159 |
35.5 Mb |
30,882 |
12.3 Mb |
|
1 kb - 10 kb | 7,998 |
12.1 Mb |
16,760 |
35.8 Mb |
|
10 kb - 100 kb | 4 |
48.1 kb |
60 |
767.5 kb |