Oryza nivara vs Oryza sativa Japonica LastZ Results

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Oryza nivara (Oryza nivara, AWHD00000000) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza nivara 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: 129,782

Genome coverage (bp) Coding exon coverage (bp)
Oryza nivara

Uncovered: 67,331,917 out of 337,950,324
Covered: 270,618,407 out of 337,950,324

Uncovered: 5,663,064 out of 42,562,444
Matches: 36,446,071 out of 42,562,444
Mismatches: 365,129 out of 42,562,444
Insertions: 88,180 out of 42,562,444

Oryza sativa Japonica Group

Uncovered: 75,660,875 out of 374,424,240
Covered: 298,763,365 out of 374,424,240

Uncovered: 3,692,220 out of 34,124,807
Matches: 29,942,773 out of 34,124,807
Mismatches: 406,671 out of 34,124,807
Insertions: 83,143 out of 34,124,807

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)