Oryza sativa Japonica Group vs Arabidopsis lyrata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) 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 82,366 alignment blocks

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

Uncovered: 345,548,011 out of 374,424,240
Covered: 28,876,229 out of 374,424,240

Uncovered: 16,289,199 out of 34,124,807
Matches: 11,536,344 out of 34,124,807
Mismatches: 5,878,330 out of 34,124,807
Insertions: 420,934 out of 34,124,807
Identity over aligned base-pairs: 64.7%

Arabidopsis lyrata

Uncovered: 187,824,233 out of 206,667,935
Covered: 18,843,702 out of 206,667,935

Uncovered: 22,202,452 out of 35,389,059
Matches: 8,605,587 out of 35,389,059
Mismatches: 4,312,853 out of 35,389,059
Insertions: 268,167 out of 35,389,059
Identity over aligned base-pairs: 65.3%