Vitis vinifera vs Ipomoea triloba LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) 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: 229,316

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

Uncovered: 430,938,265 out of 486,265,422
Covered: 55,327,157 out of 486,265,422

Uncovered: 5,156,138 out of 32,794,161
Matches: 19,078,239 out of 32,794,161
Mismatches: 7,977,415 out of 32,794,161
Insertions: 582,369 out of 32,794,161

Ipomoea triloba

Uncovered: 400,114,995 out of 461,827,428
Covered: 61,712,433 out of 461,827,428

Uncovered: 6,960,581 out of 39,533,495
Matches: 22,641,572 out of 39,533,495
Mismatches: 9,263,319 out of 39,533,495
Insertions: 668,023 out of 39,533,495

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 Ipomoea triloba
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}