Oryza nivara vs Oryza sativa Japonica Group LastZ results

Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) 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 nivara 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 129,782 alignment blocks

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

Uncovered: 67,331,917 out of 337,950,324
Covered: 270,618,407 out of 337,950,324

Uncovered: 5,663,064 out of 42,562,444
Matches: 36,446,071 out of 42,562,444
Mismatches: 365,129 out of 42,562,444
Insertions: 88,180 out of 42,562,444
Identity over aligned base-pairs: 98.8%

Oryza sativa Japonica Group

Uncovered: 75,660,875 out of 374,424,240
Covered: 298,763,365 out of 374,424,240

Uncovered: 3,692,220 out of 34,124,807
Matches: 29,942,773 out of 34,124,807
Mismatches: 406,671 out of 34,124,807
Insertions: 83,143 out of 34,124,807
Identity over aligned base-pairs: 98.4%