Vitis vinifera vs Cynara cardunculus LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) 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: 245,409

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

Uncovered: 431,779,969 out of 486,265,422
Covered: 54,485,453 out of 486,265,422

Uncovered: 5,630,102 out of 32,794,161
Matches: 18,663,661 out of 32,794,161
Mismatches: 7,869,179 out of 32,794,161
Insertions: 631,219 out of 32,794,161

Cynara cardunculus var. scolymus

Uncovered: 666,180,752 out of 724,667,265
Covered: 58,486,513 out of 724,667,265

Uncovered: 4,565,329 out of 32,068,562
Matches: 19,220,192 out of 32,068,562
Mismatches: 7,743,456 out of 32,068,562
Insertions: 539,585 out of 32,068,562

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 Cynara cardunculus
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}