Arabidopsis thaliana vs Oryza sativa Japonica Group LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. Arabidopsis thaliana 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 81,291 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 101,090,527 out of 119,667,750
Covered: 18,577,223 out of 119,667,750

Uncovered: 19,827,446 out of 33,462,323
Matches: 8,890,436 out of 33,462,323
Mismatches: 4,468,824 out of 33,462,323
Insertions: 275,617 out of 33,462,323
Identity over aligned base-pairs: 65.2%

Oryza sativa Japonica Group

Uncovered: 345,625,867 out of 374,424,240
Covered: 28,798,373 out of 374,424,240

Uncovered: 16,364,338 out of 34,124,807
Matches: 11,482,805 out of 34,124,807
Mismatches: 5,862,754 out of 34,124,807
Insertions: 414,910 out of 34,124,807
Identity over aligned base-pairs: 64.7%