Solanum lycopersicum vs Arabidopsis thaliana LastZ Results

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Solanum lycopersicum (Solanum lycopersicum str. Heinz 1706, SL2.50) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) 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: 152,097

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

Uncovered: 781,867,870 out of 823,630,941
Covered: 41,763,071 out of 823,630,941

Uncovered: 9,868,339 out of 35,320,734
Matches: 17,017,723 out of 35,320,734
Mismatches: 7,809,876 out of 35,320,734
Insertions: 624,796 out of 35,320,734

Arabidopsis thaliana

Uncovered: 84,914,632 out of 119,667,750
Covered: 34,753,118 out of 119,667,750

Uncovered: 8,557,215 out of 33,462,323
Matches: 16,685,002 out of 33,462,323
Mismatches: 7,658,620 out of 33,462,323
Insertions: 561,486 out of 33,462,323

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 Arabidopsis thaliana
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}