Vitis vinifera vs Cucumis sativus LastZ Results

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Vitis vinifera (Vitis vinifera, IGGP_12x) and Cucumis sativus (Cucumis sativus, ASM407v2) 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: 165,610

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

Uncovered: 434,891,313 out of 486,265,422
Covered: 51,374,109 out of 486,265,422

Uncovered: 6,090,973 out of 32,794,161
Matches: 18,598,803 out of 32,794,161
Mismatches: 7,613,429 out of 32,794,161
Insertions: 490,956 out of 32,794,161

Cucumis sativus

Uncovered: 155,421,691 out of 193,829,320
Covered: 38,407,629 out of 193,829,320

Uncovered: 3,469,453 out of 26,192,424
Matches: 15,920,718 out of 26,192,424
Mismatches: 6,371,214 out of 26,192,424
Insertions: 431,039 out of 26,192,424

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 Cucumis sativus
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}