Arabidopsis thaliana vs Brassica oleracea LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterArabidopsis thalianaBrassica oleracea
Chunk size10,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 362,859 alignment blocks

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
Identity over aligned base-pairs: 82.4%

Brassica 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
Identity over aligned base-pairs: 82.3%