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Oryza sativa Japonica Group vs Setaria italica LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 217,639

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

Uncovered: 291,343,280 out of 375,049,285
Covered: 83,706,005 out of 375,049,285

Uncovered: 3,094,989 out of 34,403,043
Matches: 24,558,920 out of 34,403,043
Mismatches: 5,969,560 out of 34,403,043
Insertions: 779,574 out of 34,403,043

Setaria italica

Uncovered: 314,247,099 out of 405,732,883
Covered: 91,485,784 out of 405,732,883

Uncovered: 3,755,883 out of 39,583,990
Matches: 28,062,278 out of 39,583,990
Mismatches: 6,940,255 out of 39,583,990
Insertions: 825,574 out of 39,583,990

Configuration parameters

Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
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)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Group Setaria italica
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}