Medicago truncatula vs Brassica oleracea LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula 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: 243,824

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 365,933,168 out of 412,800,391
Covered: 46,867,223 out of 412,800,391

Uncovered: 20,192,858 out of 50,132,764
Matches: 19,670,985 out of 50,132,764
Mismatches: 9,395,116 out of 50,132,764
Insertions: 873,805 out of 50,132,764

Brassica oleracea var. oleracea

Uncovered: 427,610,131 out of 488,622,507
Covered: 61,012,376 out of 488,622,507

Uncovered: 23,448,172 out of 61,722,508
Matches: 25,572,879 out of 61,722,508
Mismatches: 11,851,443 out of 61,722,508
Insertions: 850,014 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

Medicago truncatula 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}