Oryza sativa Japonica vs Brachypodium distachyon LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Brachypodium distachyon (Brachypodium distachyon, v1.0) 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: 130,854

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

Uncovered: 296,003,891 out of 374,424,240
Covered: 78,420,349 out of 374,424,240

Uncovered: 3,856,820 out of 34,124,807
Matches: 23,721,799 out of 34,124,807
Mismatches: 5,765,156 out of 34,124,807
Insertions: 781,032 out of 34,124,807

Brachypodium distachyon

Uncovered: 208,298,080 out of 271,923,306
Covered: 63,625,226 out of 271,923,306

Uncovered: 6,868,711 out of 34,177,820
Matches: 21,945,990 out of 34,177,820
Mismatches: 4,787,091 out of 34,177,820
Insertions: 576,028 out of 34,177,820

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)