Vitis vinifera vs Oryza glaberrima LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_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: 151,635

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

Uncovered: 451,945,067 out of 486,265,422
Covered: 34,320,355 out of 486,265,422

Uncovered: 11,576,747 out of 32,794,161
Matches: 13,842,115 out of 32,794,161
Mismatches: 6,919,869 out of 32,794,161
Insertions: 455,430 out of 32,794,161

Oryza glaberrima

Uncovered: 284,449,168 out of 316,419,574
Covered: 31,970,406 out of 316,419,574

Uncovered: 14,898,246 out of 36,293,721
Matches: 13,934,963 out of 36,293,721
Mismatches: 6,967,856 out of 36,293,721
Insertions: 492,656 out of 36,293,721

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 Oryza glaberrima
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}