Solanum lycopersicum vs Oryza sativa Japonica LastZ Results

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Solanum lycopersicum (Solanum lycopersicum str. Heinz 1706, SL2.50) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Solanum lycopersicum 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: 142,781

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum str. Heinz 1706

Uncovered: 789,686,665 out of 823,630,941
Covered: 33,944,276 out of 823,630,941

Uncovered: 14,686,474 out of 35,320,734
Matches: 13,441,810 out of 35,320,734
Mismatches: 6,819,027 out of 35,320,734
Insertions: 373,423 out of 35,320,734

Oryza sativa Japonica Group

Uncovered: 344,681,831 out of 374,424,240
Covered: 29,742,409 out of 374,424,240

Uncovered: 16,047,574 out of 34,124,807
Matches: 11,661,061 out of 34,124,807
Mismatches: 6,035,618 out of 34,124,807
Insertions: 380,554 out of 34,124,807

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

Solanum lycopersicum Oryza sativa Japonica
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}