Vitis vinifera vs Solanum lycopersicum LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Solanum lycopersicum (Solanum lycopersicum, SL3.0) 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: 214,156

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

Uncovered: 431,437,399 out of 486,265,422
Covered: 54,828,023 out of 486,265,422

Uncovered: 5,279,344 out of 32,794,161
Matches: 19,022,420 out of 32,794,161
Mismatches: 7,923,963 out of 32,794,161
Insertions: 568,434 out of 32,794,161

Solanum lycopersicum

Uncovered: 774,782,364 out of 827,747,456
Covered: 52,965,092 out of 827,747,456

Uncovered: 7,625,820 out of 35,932,555
Matches: 19,736,949 out of 35,932,555
Mismatches: 8,064,781 out of 35,932,555
Insertions: 505,005 out of 35,932,555

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 Solanum lycopersicum
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}