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Oryza punctata vs Oryza brachyantha LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) 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 309,205 alignment blocks

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

Uncovered: 234,774,898 out of 393,816,603
Covered: 159,041,705 out of 393,816,603

Uncovered: 3,547,891 out of 39,315,246
Matches: 30,713,000 out of 39,315,246
Mismatches: 4,332,075 out of 39,315,246
Insertions: 722,280 out of 39,315,246
Identity over aligned base-pairs: 85.9%

Oryza brachyantha

Uncovered: 150,408,631 out of 260,838,168
Covered: 110,429,537 out of 260,838,168

Uncovered: 4,598,457 out of 33,473,466
Matches: 25,612,052 out of 33,473,466
Mismatches: 2,831,505 out of 33,473,466
Insertions: 431,452 out of 33,473,466
Identity over aligned base-pairs: 88.7%