Oryza sativa Japonica vs Setaria italica LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Setaria italica (Setaria italica, JGIv2.0) 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: 139,032

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

Uncovered: 293,219,968 out of 374,424,240
Covered: 81,204,272 out of 374,424,240

Uncovered: 3,336,491 out of 34,124,807
Matches: 24,230,053 out of 34,124,807
Mismatches: 5,811,981 out of 34,124,807
Insertions: 746,282 out of 34,124,807

Setaria italica

Uncovered: 339,005,115 out of 405,737,341
Covered: 66,732,226 out of 405,737,341

Uncovered: 10,672,892 out of 39,744,767
Matches: 23,190,234 out of 39,744,767
Mismatches: 5,244,728 out of 39,744,767
Insertions: 636,913 out of 39,744,767

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)