Vitis vinifera vs Prunus persica LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 203,095

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 421,423,085 out of 486,265,422
Covered: 64,842,337 out of 486,265,422

Uncovered: 3,562,734 out of 32,794,161
Matches: 21,321,593 out of 32,794,161
Mismatches: 7,413,599 out of 32,794,161
Insertions: 496,235 out of 32,794,161

Prunus persica

Uncovered: 171,058,246 out of 227,411,381
Covered: 56,353,135 out of 227,411,381

Uncovered: 3,927,321 out of 33,236,255
Matches: 21,161,000 out of 33,236,255
Mismatches: 7,514,872 out of 33,236,255
Insertions: 633,062 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

Vitis vinifera 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}