Oryza sativa Japonica Group vs Ananas comosus LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Ananas comosus (Ananas comosus, F153) 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.


Number of alignment blocks: 152,037

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

Uncovered: 332,610,423 out of 375,049,285
Covered: 42,438,862 out of 375,049,285

Uncovered: 9,142,640 out of 34,424,450
Matches: 17,407,512 out of 34,424,450
Mismatches: 7,150,390 out of 34,424,450
Insertions: 723,908 out of 34,424,450

Ananas comosus

Uncovered: 279,872,965 out of 315,839,004
Covered: 35,966,039 out of 315,839,004

Uncovered: 5,850,447 out of 27,915,811
Matches: 15,308,581 out of 27,915,811
Mismatches: 6,181,719 out of 27,915,811
Insertions: 575,064 out of 27,915,811

Configuration parameters

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)
     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 Ananas comosus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options