Oryza glumaepatula vs Oryza nivara LastZ Results

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Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) and Oryza nivara (Oryza nivara, AWHD00000000) 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: 132,339

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

Uncovered: 113,922,314 out of 372,860,283
Covered: 258,937,969 out of 372,860,283

Uncovered: 350,759 out of 41,162,840
Matches: 39,850,744 out of 41,162,840
Mismatches: 789,326 out of 41,162,840
Insertions: 172,011 out of 41,162,840

Oryza nivara

Uncovered: 93,879,033 out of 337,950,324
Covered: 244,071,291 out of 337,950,324

Uncovered: 3,254,201 out of 42,480,949
Matches: 38,552,111 out of 42,480,949
Mismatches: 545,369 out of 42,480,949
Insertions: 129,268 out of 42,480,949

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 nivara
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}