Vitis vinifera vs Helianthus annuus LastZ Results

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Vitis vinifera (Vitis vinifera, IGGP_12x) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) 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: 427,684

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

Uncovered: 429,487,858 out of 486,265,422
Covered: 56,777,564 out of 486,265,422

Uncovered: 5,868,706 out of 32,794,161
Matches: 18,040,636 out of 32,794,161
Mismatches: 8,109,591 out of 32,794,161
Insertions: 775,228 out of 32,794,161

Helianthus annuus

Uncovered: 2,902,182,699 out of 3,027,844,945
Covered: 125,662,246 out of 3,027,844,945

Uncovered: 12,509,694 out of 54,343,734
Matches: 28,704,360 out of 54,343,734
Mismatches: 12,374,279 out of 54,343,734
Insertions: 755,401 out of 54,343,734

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 Helianthus annuus
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}