Oryza sativa Japonica Group vs Solanum lycopersicum LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Solanum lycopersicum (Solanum lycopersicum, SL3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 140,336

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 344,760,716 out of 375,049,285
Covered: 30,288,569 out of 375,049,285

Uncovered: 15,781,338 out of 34,403,043
Matches: 11,965,326 out of 34,403,043
Mismatches: 6,262,874 out of 34,403,043
Insertions: 393,505 out of 34,403,043

Solanum lycopersicum

Uncovered: 796,901,535 out of 827,747,456
Covered: 30,845,921 out of 827,747,456

Uncovered: 15,582,487 out of 35,932,555
Matches: 13,231,972 out of 35,932,555
Mismatches: 6,743,906 out of 35,932,555
Insertions: 374,190 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

Oryza sativa Japonica Group 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}