Oryza sativa Japonica vs Sorghum bicolor LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Sorghum bicolor (Sorghum bicolor, Sorbi1) 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.


Number of alignment blocks: 132,530

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

Uncovered: 299,888,197 out of 374,424,240
Covered: 74,536,043 out of 374,424,240

Uncovered: 3,745,501 out of 34,124,807
Matches: 23,717,969 out of 34,124,807
Mismatches: 5,955,578 out of 34,124,807
Insertions: 705,759 out of 34,124,807

Sorghum bicolor

Uncovered: 678,109,501 out of 738,540,932
Covered: 60,431,431 out of 738,540,932

Uncovered: 12,196,717 out of 40,003,363
Matches: 21,964,647 out of 40,003,363
Mismatches: 5,141,073 out of 40,003,363
Insertions: 700,926 out of 40,003,363

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
Other parameters (other)