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Oryza sativa Japonica Group vs Capsicum annuum LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Capsicum annuum (Capsicum annuum, ASM51225v2) 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: 191,256

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

Uncovered: 344,375,458 out of 375,049,285
Covered: 30,673,827 out of 375,049,285

Uncovered: 15,591,192 out of 34,424,450
Matches: 12,039,303 out of 34,424,450
Mismatches: 6,387,052 out of 34,424,450
Insertions: 406,903 out of 34,424,450

Capsicum annuum

Uncovered: 3,019,723,690 out of 3,063,864,880
Covered: 44,141,190 out of 3,063,864,880

Uncovered: 17,327,991 out of 39,113,865
Matches: 14,165,326 out of 39,113,865
Mismatches: 7,213,030 out of 39,113,865
Insertions: 407,518 out of 39,113,865

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 Capsicum annuum
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}