Vitis vinifera vs Capsicum annuum LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Capsicum annuum (Capsicum annuum, ASM51225v2) 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: 324,914

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

Uncovered: 429,486,190 out of 486,265,422
Covered: 56,779,232 out of 486,265,422

Uncovered: 5,237,428 out of 32,794,161
Matches: 18,955,396 out of 32,794,161
Mismatches: 8,038,895 out of 32,794,161
Insertions: 562,442 out of 32,794,161

Capsicum annuum

Uncovered: 2,976,246,158 out of 3,063,864,880
Covered: 87,618,722 out of 3,063,864,880

Uncovered: 9,403,443 out of 39,113,865
Matches: 20,665,699 out of 39,113,865
Mismatches: 8,505,331 out of 39,113,865
Insertions: 539,392 out of 39,113,865

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 Capsicum annuum
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}