Oryza sativa Japonica Group vs Selaginella moellendorffii LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Selaginella moellendorffii (Selaginella moellendorffii, v1.0) 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 62,566 alignment blocks

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

Uncovered: 354,281,791 out of 374,424,240
Covered: 20,142,449 out of 374,424,240

Uncovered: 20,406,463 out of 34,124,807
Matches: 8,726,635 out of 34,124,807
Mismatches: 4,576,191 out of 34,124,807
Insertions: 415,518 out of 34,124,807
Identity over aligned base-pairs: 63.6%

Selaginella moellendorffii

Uncovered: 200,615,953 out of 212,645,483
Covered: 12,029,530 out of 212,645,483

Uncovered: 32,232,322 out of 41,155,148
Matches: 5,710,066 out of 41,155,148
Mismatches: 3,000,305 out of 41,155,148
Insertions: 212,455 out of 41,155,148
Identity over aligned base-pairs: 64.0%