Oryza sativa Japonica Group vs Brassica rapa LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Brassica rapa (Brassica rapa, Brapa_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 89,504 alignment blocks

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

Uncovered: 344,202,788 out of 374,424,240
Covered: 30,221,452 out of 374,424,240

Uncovered: 15,465,464 out of 34,124,807
Matches: 12,078,031 out of 34,124,807
Mismatches: 6,076,580 out of 34,124,807
Insertions: 504,732 out of 34,124,807
Identity over aligned base-pairs: 64.7%

Brassica rapa

Uncovered: 263,352,597 out of 283,822,783
Covered: 20,470,186 out of 283,822,783

Uncovered: 33,375,384 out of 48,055,850
Matches: 9,596,582 out of 48,055,850
Mismatches: 4,770,934 out of 48,055,850
Insertions: 312,950 out of 48,055,850
Identity over aligned base-pairs: 65.4%