Solanum lycopersicum vs Nicotiana attenuata LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) 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: 466,411

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

Uncovered: 682,098,793 out of 827,747,456
Covered: 145,648,663 out of 827,747,456

Uncovered: 6,763,697 out of 35,932,555
Matches: 24,760,184 out of 35,932,555
Mismatches: 4,053,158 out of 35,932,555
Insertions: 355,516 out of 35,932,555

Nicotiana attenuata

Uncovered: 2,049,846,317 out of 2,365,682,703
Covered: 315,836,386 out of 2,365,682,703

Uncovered: 7,281,589 out of 37,106,589
Matches: 25,215,616 out of 37,106,589
Mismatches: 4,109,732 out of 37,106,589
Insertions: 499,652 out of 37,106,589

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 Nicotiana attenuata
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}