Oryza sativa Japonica vs Oryza rufipogon LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. 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: 103,093

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

Uncovered: 70,757,579 out of 373,245,519
Covered: 302,487,940 out of 373,245,519

Uncovered: 337,005 out of 44,520,596
Matches: 43,620,233 out of 44,520,596
Mismatches: 445,769 out of 44,520,596
Insertions: 117,589 out of 44,520,596

Oryza rufipogon

Uncovered: 51,237,990 out of 338,040,714
Covered: 286,802,724 out of 338,040,714

Uncovered: 1,152,224 out of 42,764,129
Matches: 41,374,852 out of 42,764,129
Mismatches: 185,533 out of 42,764,129
Insertions: 51,520 out of 42,764,129

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 Oryza rufipogon
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}