Arabidopsis thaliana vs Brassica oleracea LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica oleracea (Brassica oleracea var. oleracea, v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 74. Arabidopsis thaliana 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: 362,859

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 41,657,572 out of 119,667,750
Covered: 78,010,178 out of 119,667,750

Uncovered: 1,015,255 out of 33,462,323
Matches: 26,731,720 out of 33,462,323
Mismatches: 4,938,695 out of 33,462,323
Insertions: 776,653 out of 33,462,323

Brassica oleracea var. oleracea

Uncovered: 318,079,695 out of 488,622,507
Covered: 170,542,812 out of 488,622,507

Uncovered: 8,501,128 out of 61,722,508
Matches: 43,789,668 out of 61,722,508
Mismatches: 8,585,120 out of 61,722,508
Insertions: 846,592 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

Arabidopsis thaliana 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}