Solanum lycopersicum vs Capsicum annuum LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Capsicum annuum (Capsicum annuum, ASM51225v2) 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: 782,928

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

Uncovered: 653,364,965 out of 827,747,456
Covered: 174,382,491 out of 827,747,456

Uncovered: 5,906,138 out of 36,416,191
Matches: 26,454,733 out of 36,416,191
Mismatches: 3,692,161 out of 36,416,191
Insertions: 363,159 out of 36,416,191

Capsicum annuum

Uncovered: 2,548,778,207 out of 3,063,864,880
Covered: 515,086,673 out of 3,063,864,880

Uncovered: 7,250,930 out of 39,113,865
Matches: 27,423,690 out of 39,113,865
Mismatches: 3,995,841 out of 39,113,865
Insertions: 443,404 out of 39,113,865

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 Capsicum annuum
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}