Vitis vinifera vs Theobroma cacao LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) 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: 182,206

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

Uncovered: 420,451,222 out of 486,265,422
Covered: 65,814,200 out of 486,265,422

Uncovered: 3,434,423 out of 32,794,161
Matches: 21,390,846 out of 32,794,161
Mismatches: 7,491,543 out of 32,794,161
Insertions: 477,349 out of 32,794,161

Theobroma cacao

Uncovered: 271,676,860 out of 324,719,311
Covered: 53,042,451 out of 324,719,311

Uncovered: 2,850,615 out of 29,183,654
Matches: 19,157,092 out of 29,183,654
Mismatches: 6,710,797 out of 29,183,654
Insertions: 465,150 out of 29,183,654

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 Theobroma cacao
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}