Arabidopsis thaliana vs Helianthus annuus LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 240,077

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 84,324,102 out of 119,667,750
Covered: 35,343,648 out of 119,667,750

Uncovered: 9,589,180 out of 33,775,569
Matches: 15,747,468 out of 33,775,569
Mismatches: 7,739,306 out of 33,775,569
Insertions: 699,615 out of 33,775,569

Helianthus annuus

Uncovered: 2,956,783,382 out of 3,027,844,945
Covered: 71,061,563 out of 3,027,844,945

Uncovered: 18,241,125 out of 54,343,734
Matches: 23,980,309 out of 54,343,734
Mismatches: 11,337,645 out of 54,343,734
Insertions: 784,655 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

Arabidopsis thaliana Helianthus annuus
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}