Oryza sativa Japonica Group vs Brassica oleracea LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) 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: 183,774

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

Uncovered: 343,255,323 out of 375,049,285
Covered: 31,793,962 out of 375,049,285

Uncovered: 14,983,511 out of 34,403,043
Matches: 12,425,763 out of 34,403,043
Mismatches: 6,424,232 out of 34,403,043
Insertions: 569,537 out of 34,403,043

Brassica oleracea var. oleracea

Uncovered: 444,059,447 out of 488,622,507
Covered: 44,563,060 out of 488,622,507

Uncovered: 30,820,499 out of 61,722,508
Matches: 20,249,026 out of 61,722,508
Mismatches: 10,055,523 out of 61,722,508
Insertions: 597,460 out of 61,722,508

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 Brassica oleracea
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}