Arabidopsis thaliana vs Prunus avium LastZ Results

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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 . Arabidopsis thaliana 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: 134,988

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 82,742,220 out of 119,667,750
Covered: 36,925,530 out of 119,667,750

Uncovered: 7,901,674 out of 33,775,569
Matches: 17,544,272 out of 33,775,569
Mismatches: 7,797,978 out of 33,775,569
Insertions: 531,645 out of 33,775,569

Prunus avium

Uncovered: 230,910,175 out of 272,361,615
Covered: 41,451,440 out of 272,361,615

Uncovered: 16,682,088 out of 38,693,511
Matches: 14,740,843 out of 38,693,511
Mismatches: 6,600,778 out of 38,693,511
Insertions: 669,802 out of 38,693,511

Configuration parameters

ParameterValue
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
Other parameters (other)--ambiguous=iupac

Chunking parameters

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}