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Oryza punctata vs Oryza glumipatula LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza punctata was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Statistics over 418,810 alignment blocks

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
Identity over aligned base-pairs: 92.6%

Oryza glumipatula

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
Identity over aligned base-pairs: 93.0%