Solanum lycopersicum vs Daucus carota LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) 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: 234,747

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

Uncovered: 768,628,757 out of 827,747,456
Covered: 59,118,699 out of 827,747,456

Uncovered: 8,069,537 out of 35,932,555
Matches: 19,157,491 out of 35,932,555
Mismatches: 8,100,909 out of 35,932,555
Insertions: 604,618 out of 35,932,555

Daucus carota subsp. sativus

Uncovered: 358,111,769 out of 421,502,825
Covered: 63,391,056 out of 421,502,825

Uncovered: 8,682,844 out of 38,118,360
Matches: 20,316,264 out of 38,118,360
Mismatches: 8,501,618 out of 38,118,360
Insertions: 617,634 out of 38,118,360

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 Daucus carota
Chunk size 10,100,000 10,100,000
Overlap 100,000 100,000
Group set size 10,100,000 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}