Oryza sativa Japonica Group vs Beta vulgaris LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Beta vulgaris (Beta vulgaris subsp. vulgaris, RefBeet-1.2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 123,504

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 345,716,257 out of 375,049,285
Covered: 29,333,028 out of 375,049,285

Uncovered: 16,300,113 out of 34,403,043
Matches: 11,641,764 out of 34,403,043
Mismatches: 6,093,203 out of 34,403,043
Insertions: 367,963 out of 34,403,043

Beta vulgaris subsp. vulgaris

Uncovered: 540,827,117 out of 566,181,630
Covered: 25,354,513 out of 566,181,630

Uncovered: 12,325,855 out of 28,257,705
Matches: 10,334,427 out of 28,257,705
Mismatches: 5,287,948 out of 28,257,705
Insertions: 309,475 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

Oryza sativa Japonica Group 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}