Arabidopsis thaliana vs Prunus dulcis LastZ results
Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus dulcis (Prunus dulcis, ALMONDv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Arabidopsis thaliana 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 | Arabidopsis thaliana | Prunus dulcis |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options |
Statistics over 127,490 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Arabidopsis thaliana |
Uncovered: 83,164,320 out of 119,667,750 |
Uncovered: 7,989,733 out of 33,775,569 |
Prunus dulcis |
Uncovered: 188,425,367 out of 227,498,357 |
Uncovered: 9,826,657 out of 33,980,404 |
Block size distribution
Size range | All 127,490 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,170 |
6.6 kb |
|||
10 bp - 100 bp | 18,625 |
1.2 Mb |
3,686 |
258.9 kb |
|
100 bp - 1 kb | 96,273 |
34.4 Mb |
21,329 |
8.4 Mb |
|
1 kb - 10 kb | 11,416 |
17.4 Mb |
14,005 |
34.2 Mb |
|
10 kb - 100 kb | 6 |
83.2 kb |
508 |
9.6 Mb |
|
100 kb - 1 Mb | 4 |
713.5 kb |