Arabidopsis thaliana vs Beta vulgaris LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Beta vulgaris (Beta vulgaris subsp. vulgaris, RefBeet-1.2.2) 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: 123,292

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

Uncovered: 88,600,055 out of 119,667,750
Covered: 31,067,695 out of 119,667,750

Uncovered: 10,807,871 out of 33,775,569
Matches: 15,352,309 out of 33,775,569
Mismatches: 7,142,768 out of 33,775,569
Insertions: 472,621 out of 33,775,569

Beta vulgaris subsp. vulgaris

Uncovered: 535,031,763 out of 566,181,630
Covered: 31,149,867 out of 566,181,630

Uncovered: 9,535,674 out of 28,257,705
Matches: 12,454,561 out of 28,257,705
Mismatches: 5,792,775 out of 28,257,705
Insertions: 474,695 out of 28,257,705

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 Beta vulgaris
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}