Oryza punctata vs Oryza nivara LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) 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

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Statistics over 421,205 alignment blocks

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

Uncovered: 164,013,098 out of 393,816,603
Covered: 229,803,505 out of 393,816,603

Uncovered: 732,137 out of 39,315,246
Matches: 35,784,508 out of 39,315,246
Mismatches: 2,340,186 out of 39,315,246
Insertions: 458,415 out of 39,315,246
Identity over aligned base-pairs: 92.7%

Oryza nivara

Uncovered: 170,524,811 out of 337,950,324
Covered: 167,425,513 out of 337,950,324

Uncovered: 6,804,216 out of 42,562,444
Matches: 33,235,391 out of 42,562,444
Mismatches: 1,993,260 out of 42,562,444
Insertions: 529,577 out of 42,562,444
Identity over aligned base-pairs: 92.9%