Vitis vinifera vs Brassica oleracea LastZ results

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 94. Vitis vinifera 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

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

Chunking parameters

ParameterVitis viniferaBrassica oleracea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 253,927 alignment blocks

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
Identity over aligned base-pairs: 66.3%

Brassica 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
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 253,927 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,823
9.9 kb
2
13.0 bp
10 bp - 100 bp
43,473
3.0 Mb
13,015
936.6 kb
100 bp - 1 kb
195,161
62.5 Mb
68,490
25.3 Mb
1 kb - 10 kb
13,432
20.7 Mb
26,772
57.8 Mb
10 kb - 100 kb
38
779.2 kb
190
2.9 Mb