Oryza sativa Japonica Group vs Solanum tuberosum LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Solanum tuberosum (Solanum tuberosum, SolTub_3.0) 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 93,926 alignment blocks

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

Uncovered: 345,141,586 out of 374,424,240
Covered: 29,282,654 out of 374,424,240

Uncovered: 15,951,901 out of 34,124,807
Matches: 11,778,067 out of 34,124,807
Mismatches: 6,026,431 out of 34,124,807
Insertions: 368,408 out of 34,124,807
Identity over aligned base-pairs: 64.8%

Solanum tuberosum

Uncovered: 790,714,661 out of 810,654,046
Covered: 19,939,385 out of 810,654,046

Uncovered: 25,526,208 out of 36,745,425
Matches: 7,291,015 out of 36,745,425
Mismatches: 3,704,180 out of 36,745,425
Insertions: 224,022 out of 36,745,425
Identity over aligned base-pairs: 65.0%