Vitis vinifera vs Trifolium pratense LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Trifolium pratense (Trifolium pratense, Trpr) 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: 211,702

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

Uncovered: 426,878,145 out of 486,265,422
Covered: 59,387,277 out of 486,265,422

Uncovered: 5,583,688 out of 32,794,161
Matches: 18,411,019 out of 32,794,161
Mismatches: 8,222,870 out of 32,794,161
Insertions: 576,584 out of 32,794,161

Trifolium pratense

Uncovered: 250,634,720 out of 304,842,038
Covered: 54,207,318 out of 304,842,038

Uncovered: 10,632,350 out of 41,242,947
Matches: 21,015,106 out of 41,242,947
Mismatches: 8,971,698 out of 41,242,947
Insertions: 623,793 out of 41,242,947

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 Trifolium pratense
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}