Oryza sativa Japonica Group vs Cyanidioschyzon merolae LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D, ASM9120v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. Oryza sativa Japonica Group 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 6,318 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 372,896,529 out of 374,424,240
Covered: 1,527,711 out of 374,424,240

Uncovered: 32,982,033 out of 34,124,807
Matches: 718,187 out of 34,124,807
Mismatches: 398,882 out of 34,124,807
Insertions: 25,705 out of 34,124,807
Identity over aligned base-pairs: 62.8%

Cyanidioschyzon merolae

Uncovered: 16,054,314 out of 16,728,945
Covered: 674,631 out of 16,728,945

Uncovered: 6,833,165 out of 7,493,795
Matches: 411,286 out of 7,493,795
Mismatches: 232,994 out of 7,493,795
Insertions: 16,350 out of 7,493,795
Identity over aligned base-pairs: 62.3%