Oryza punctata vs Oryza sativa Japonica Group LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) 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 843,843 alignment blocks

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

Uncovered: 159,679,307 out of 393,816,603
Covered: 234,137,296 out of 393,816,603

Uncovered: 637,642 out of 39,315,246
Matches: 35,821,623 out of 39,315,246
Mismatches: 2,376,181 out of 39,315,246
Insertions: 479,800 out of 39,315,246
Identity over aligned base-pairs: 92.6%

Oryza sativa Japonica Group

Uncovered: 140,715,651 out of 374,424,240
Covered: 233,708,589 out of 374,424,240

Uncovered: 778,990 out of 34,124,807
Matches: 30,757,922 out of 34,124,807
Mismatches: 2,112,070 out of 34,124,807
Insertions: 475,825 out of 34,124,807
Identity over aligned base-pairs: 92.2%