Vitis vinifera vs Oryza brachyantha LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 149,462

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 450,338,649 out of 486,265,422
Covered: 35,926,773 out of 486,265,422

Uncovered: 11,168,333 out of 32,794,161
Matches: 13,922,074 out of 32,794,161
Mismatches: 7,257,306 out of 32,794,161
Insertions: 446,448 out of 32,794,161

Oryza brachyantha

Uncovered: 230,055,725 out of 260,838,168
Covered: 30,782,443 out of 260,838,168

Uncovered: 12,859,417 out of 33,473,466
Matches: 13,445,422 out of 33,473,466
Mismatches: 6,749,793 out of 33,473,466
Insertions: 418,834 out of 33,473,466

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

Vitis vinifera Oryza brachyantha
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}