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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

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

ParameterArabidopsis thalianaBrassica oleracea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
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: 1,071,576 out of 33,775,569
Matches: 26,902,394 out of 33,775,569
Mismatches: 4,996,731 out of 33,775,569
Insertions: 804,868 out of 33,775,569
Identity over aligned base-pairs: 82.3%

Brassica oleracea

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

Uncovered: 8,502,447 out of 61,722,508
Matches: 43,788,868 out of 61,722,508
Mismatches: 8,584,598 out of 61,722,508
Insertions: 846,595 out of 61,722,508
Identity over aligned base-pairs: 82.3%

Block size distribution

Size range All 362,859 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,222
26.0 kb
10 bp - 100 bp
72,211
4.0 Mb
18,451
1.3 Mb
100 bp - 1 kb
229,713
89.2 Mb
88,750
32.9 Mb
1 kb - 10 kb
56,703
105.9 Mb
23,615
54.5 Mb
10 kb - 100 kb
10
112.9 kb
263
6.5 Mb
100 kb - 1 Mb
75
24.4 Mb
1 Mb - 10 Mb
31
79.7 Mb