Arabidopsis thaliana vs Prunus persica LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) 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: 127,079

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

Uncovered: 83,147,367 out of 119,667,750
Covered: 36,520,383 out of 119,667,750

Uncovered: 7,873,151 out of 33,775,569
Matches: 17,697,132 out of 33,775,569
Mismatches: 7,671,864 out of 33,775,569
Insertions: 533,422 out of 33,775,569

Prunus persica

Uncovered: 188,954,612 out of 227,411,381
Covered: 38,456,769 out of 227,411,381

Uncovered: 8,548,783 out of 33,236,255
Matches: 16,577,933 out of 33,236,255
Mismatches: 7,395,024 out of 33,236,255
Insertions: 714,515 out of 33,236,255

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 persica
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}