Brassica rapa vs Brassica oleracea LastZ results

Brassica rapa (Brassica rapa, Brapa_1.0) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Brassica rapa 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

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

Statistics over 1,134,713 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Brassica rapa

Uncovered: 44,565,284 out of 283,822,783
Covered: 239,257,499 out of 283,822,783

Uncovered: 1,673,164 out of 48,055,850
Matches: 44,005,632 out of 48,055,850
Mismatches: 2,069,699 out of 48,055,850
Insertions: 307,355 out of 48,055,850
Identity over aligned base-pairs: 94.9%

Brassica oleracea

Uncovered: 68,997,646 out of 488,622,507
Covered: 419,624,861 out of 488,622,507

Uncovered: 1,103,315 out of 61,722,508
Matches: 55,952,450 out of 61,722,508
Mismatches: 4,070,676 out of 61,722,508
Insertions: 596,067 out of 61,722,508
Identity over aligned base-pairs: 92.3%