Oryza punctata vs Oryza glumaepatula LastZ Results

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Oryza punctata (Oryza punctata, AVCL00000000) and Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza punctata 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: 418,810

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

Uncovered: 164,502,501 out of 393,816,603
Covered: 229,314,102 out of 393,816,603

Uncovered: 794,403 out of 39,315,246
Matches: 35,686,756 out of 39,315,246
Mismatches: 2,368,477 out of 39,315,246
Insertions: 465,610 out of 39,315,246

Oryza glumaepatula

Uncovered: 206,416,721 out of 372,860,283
Covered: 166,443,562 out of 372,860,283

Uncovered: 6,021,754 out of 41,246,944
Matches: 32,767,432 out of 41,246,944
Mismatches: 1,936,251 out of 41,246,944
Insertions: 521,507 out of 41,246,944

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)