Solanum lycopersicum vs Solanum tuberosum LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Solanum tuberosum (Solanum tuberosum, SolTub_3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 591,651

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 487,424,150 out of 827,747,456
Covered: 340,323,306 out of 827,747,456

Uncovered: 2,138,381 out of 35,932,555
Matches: 31,317,979 out of 35,932,555
Mismatches: 2,311,189 out of 35,932,555
Insertions: 165,006 out of 35,932,555

Solanum tuberosum

Uncovered: 483,293,563 out of 810,654,046
Covered: 327,360,483 out of 810,654,046

Uncovered: 5,770,147 out of 36,745,425
Matches: 28,463,158 out of 36,745,425
Mismatches: 2,197,996 out of 36,745,425
Insertions: 314,124 out of 36,745,425

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 --matchcount=1000

Chunking parameters

Solanum lycopersicum Solanum tuberosum
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}