Vitis vinifera vs Camelina sativa LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Camelina sativa (Camelina sativa, Cs) 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: 430,618

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

Uncovered: 423,727,998 out of 486,265,422
Covered: 62,537,424 out of 486,265,422

Uncovered: 6,702,342 out of 32,794,161
Matches: 16,809,321 out of 32,794,161
Mismatches: 8,604,751 out of 32,794,161
Insertions: 677,747 out of 32,794,161

Camelina sativa

Uncovered: 514,799,882 out of 641,356,059
Covered: 126,556,177 out of 641,356,059

Uncovered: 29,973,638 out of 107,028,261
Matches: 52,327,635 out of 107,028,261
Mismatches: 23,137,476 out of 107,028,261
Insertions: 1,589,512 out of 107,028,261

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 Camelina sativa
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options