Oryza sativa Japonica vs Zea mays LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Zea mays (Zea mays, AGPv3) 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: 133,321

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

Uncovered: 308,180,164 out of 374,424,240
Covered: 66,244,076 out of 374,424,240

Uncovered: 4,951,574 out of 34,124,807
Matches: 22,530,836 out of 34,124,807
Mismatches: 5,905,610 out of 34,124,807
Insertions: 736,787 out of 34,124,807

Zea mays

Uncovered: 2,015,279,359 out of 2,067,864,162
Covered: 52,584,803 out of 2,067,864,162

Uncovered: 18,593,535 out of 44,177,667
Matches: 20,106,991 out of 44,177,667
Mismatches: 4,845,267 out of 44,177,667
Insertions: 631,874 out of 44,177,667

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)