Oryza glumaepatula vs Oryza rufipogon LastZ Results

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Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glumaepatula 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: 146,436

Genome coverage (bp) Coding exon coverage (bp)
Oryza glumaepatula

Uncovered: 113,576,679 out of 372,860,283
Covered: 259,283,604 out of 372,860,283

Uncovered: 306,007 out of 41,162,840
Matches: 39,896,681 out of 41,162,840
Mismatches: 778,336 out of 41,162,840
Insertions: 181,816 out of 41,162,840

Oryza rufipogon

Uncovered: 92,964,917 out of 338,040,714
Covered: 245,075,797 out of 338,040,714

Uncovered: 3,368,235 out of 42,764,129
Matches: 38,713,170 out of 42,764,129
Mismatches: 545,110 out of 42,764,129
Insertions: 137,614 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 glumaepatula 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}