Oryza sativa Japonica vs Selaginella moellendorffii LastZ Results

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Oryza sativa Japonica (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 76. Oryza sativa Japonica was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 62,566

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

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

Configuration parameters

ParameterValue
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)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)