Prunus persica vs Oryza sativa Japonica LastZ Results

Back to all analyses

Prunus persica (Prunus persica, Prupe1_0) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Prunus persica 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: 144,381

Genome coverage (bp) Coding exon coverage (bp)
Prunus persica

Uncovered: 192,930,078 out of 227,251,827
Covered: 34,321,749 out of 227,251,827

Uncovered: 12,752,542 out of 33,830,599
Matches: 13,727,229 out of 33,830,599
Mismatches: 6,868,035 out of 33,830,599
Insertions: 482,793 out of 33,830,599

Oryza sativa Japonica Group

Uncovered: 341,273,281 out of 374,424,240
Covered: 33,150,959 out of 374,424,240

Uncovered: 13,998,143 out of 34,124,807
Matches: 13,153,696 out of 34,124,807
Mismatches: 6,500,067 out of 34,124,807
Insertions: 472,901 out of 34,124,807

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Prunus persica Oryza sativa Japonica
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}