Vitis vinifera vs Theobroma cacao Matina 1-6 LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Theobroma cacao Matina 1-6 (Theobroma cacao, Theobroma_cacao_20110822) 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: 182,734

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

Uncovered: 419,868,641 out of 486,265,422
Covered: 66,396,781 out of 486,265,422

Uncovered: 3,411,321 out of 32,794,161
Matches: 21,383,281 out of 32,794,161
Mismatches: 7,521,745 out of 32,794,161
Insertions: 477,814 out of 32,794,161

Theobroma cacao

Uncovered: 292,657,403 out of 345,993,675
Covered: 53,336,272 out of 345,993,675

Uncovered: 6,601,058 out of 34,800,751
Matches: 20,369,885 out of 34,800,751
Mismatches: 7,295,151 out of 34,800,751
Insertions: 534,657 out of 34,800,751

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 Matina 1-6
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options