Arabidopsis thaliana vs Solanum lycopersicum LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Solanum lycopersicum (Solanum lycopersicum, SL3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 140,482

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 86,133,126 out of 119,667,750
Covered: 33,534,624 out of 119,667,750

Uncovered: 9,617,505 out of 33,775,569
Matches: 16,129,072 out of 33,775,569
Mismatches: 7,480,633 out of 33,775,569
Insertions: 548,359 out of 33,775,569

Solanum lycopersicum

Uncovered: 789,442,701 out of 827,747,456
Covered: 38,304,755 out of 827,747,456

Uncovered: 11,599,929 out of 35,932,555
Matches: 16,244,367 out of 35,932,555
Mismatches: 7,485,131 out of 35,932,555
Insertions: 603,128 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

Arabidopsis thaliana 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}