Solanum lycopersicum vs Helianthus annuus LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) 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: 463,312

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

Uncovered: 763,183,339 out of 827,747,456
Covered: 64,564,117 out of 827,747,456

Uncovered: 8,659,175 out of 35,932,555
Matches: 18,237,324 out of 35,932,555
Mismatches: 8,242,284 out of 35,932,555
Insertions: 793,772 out of 35,932,555

Helianthus annuus

Uncovered: 2,875,648,807 out of 3,027,844,945
Covered: 152,196,138 out of 3,027,844,945

Uncovered: 13,046,464 out of 54,343,734
Matches: 28,155,573 out of 54,343,734
Mismatches: 12,328,200 out of 54,343,734
Insertions: 813,497 out of 54,343,734

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 Helianthus annuus
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}