Oryza sativa Japonica vs Glycine max LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Glycine max (Glycine max, V1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica 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: 103,673

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

Uncovered: 341,670,352 out of 374,424,240
Covered: 32,753,888 out of 374,424,240

Uncovered: 14,550,078 out of 34,124,807
Matches: 12,798,659 out of 34,124,807
Mismatches: 6,290,577 out of 34,124,807
Insertions: 485,493 out of 34,124,807

Glycine max

Uncovered: 948,746,442 out of 973,344,380
Covered: 24,597,938 out of 973,344,380

Uncovered: 47,683,486 out of 64,476,920
Matches: 11,046,044 out of 64,476,920
Mismatches: 5,359,340 out of 64,476,920
Insertions: 388,050 out of 64,476,920

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 Glycine max
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}