Vitis vinifera vs Brassica oleracea LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 253,927

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 440,174,665 out of 486,265,422
Covered: 46,090,757 out of 486,265,422

Uncovered: 7,421,047 out of 32,794,161
Matches: 16,814,112 out of 32,794,161
Mismatches: 7,826,082 out of 32,794,161
Insertions: 732,920 out of 32,794,161

Brassica oleracea var. oleracea

Uncovered: 426,870,523 out of 488,622,507
Covered: 61,751,984 out of 488,622,507

Uncovered: 22,328,061 out of 61,722,508
Matches: 26,695,649 out of 61,722,508
Mismatches: 11,909,678 out of 61,722,508
Insertions: 789,120 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

Vitis vinifera 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}