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Vitis vinifera vs Saccharum spontaneum LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) 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: 594,172

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

Uncovered: 447,014,651 out of 486,265,422
Covered: 39,250,771 out of 486,265,422

Uncovered: 10,104,150 out of 32,794,161
Matches: 14,740,017 out of 32,794,161
Mismatches: 7,422,332 out of 32,794,161
Insertions: 527,662 out of 32,794,161

Saccharum spontaneum

Uncovered: 2,729,909,429 out of 2,900,240,836
Covered: 170,331,407 out of 2,900,240,836

Uncovered: 23,241,196 out of 62,027,027
Matches: 25,430,375 out of 62,027,027
Mismatches: 12,477,803 out of 62,027,027
Insertions: 877,653 out of 62,027,027

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 Saccharum spontaneum
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}