Vitis vinifera vs Triticum turgidum LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Triticum turgidum (Triticum turgidum, Svevo.v1) 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: 488,424

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

Uncovered: 446,396,374 out of 486,265,422
Covered: 39,869,048 out of 486,265,422

Uncovered: 10,075,293 out of 32,794,161
Matches: 14,640,650 out of 32,794,161
Mismatches: 7,550,350 out of 32,794,161
Insertions: 527,868 out of 32,794,161

Triticum turgidum

Uncovered: 10,319,666,298 out of 10,463,058,104
Covered: 143,391,806 out of 10,463,058,104

Uncovered: 35,718,003 out of 88,577,667
Matches: 34,081,385 out of 88,577,667
Mismatches: 17,498,386 out of 88,577,667
Insertions: 1,279,893 out of 88,577,667

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 Triticum turgidum
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}