Oryza sativa Japonica Group vs Vigna angularis LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Vigna angularis (Vigna angularis, Vigan1.1) 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: 149,005

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

Uncovered: 342,676,222 out of 375,049,285
Covered: 32,373,063 out of 375,049,285

Uncovered: 14,305,021 out of 34,403,043
Matches: 13,004,823 out of 34,403,043
Mismatches: 6,575,119 out of 34,403,043
Insertions: 518,080 out of 34,403,043

Vigna angularis

Uncovered: 433,220,647 out of 466,744,453
Covered: 33,523,806 out of 466,744,453

Uncovered: 17,005,442 out of 37,822,470
Matches: 13,600,080 out of 37,822,470
Mismatches: 6,779,830 out of 37,822,470
Insertions: 437,118 out of 37,822,470

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Vigna angularis
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}