Oryza sativa Japonica Group vs Prunus persica LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 135,742

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 341,457,938 out of 375,049,285
Covered: 33,591,347 out of 375,049,285

Uncovered: 13,680,784 out of 34,403,043
Matches: 13,504,208 out of 34,403,043
Mismatches: 6,726,159 out of 34,403,043
Insertions: 491,892 out of 34,403,043

Prunus persica

Uncovered: 196,387,515 out of 227,411,381
Covered: 31,023,866 out of 227,411,381

Uncovered: 12,239,021 out of 33,236,255
Matches: 13,677,817 out of 33,236,255
Mismatches: 6,834,782 out of 33,236,255
Insertions: 484,635 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

Oryza sativa Japonica Group 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}