Arabidopsis thaliana vs Prunus avium LastZ results
Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus avium (Prunus avium, PAV_r1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 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 134,988 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Arabidopsis thaliana |
Uncovered: 82,742,220 out of 119,667,750 |
Uncovered: 7,901,674 out of 33,775,569 |
Prunus avium |
Uncovered: 230,910,175 out of 272,361,615 |
Uncovered: 16,682,088 out of 38,693,511 |
Block size distribution
Size range | All 134,988 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,294 |
7.3 kb |
|||
10 bp - 100 bp | 19,824 |
1.3 Mb |
4,259 |
302.1 kb |
|
100 bp - 1 kb | 102,139 |
36.4 Mb |
24,920 |
9.7 Mb |
|
1 kb - 10 kb | 11,723 |
18.1 Mb |
15,174 |
36.8 Mb |
|
10 kb - 100 kb | 8 |
93.8 kb |
497 |
8.9 Mb |
|
100 kb - 1 Mb | 1 |
127.0 kb |