Oryza sativa Japonica vs Populus trichocarpa LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Populus trichocarpa (Populus trichocarpa, JGI2.0) 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: 97,229

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

Uncovered: 342,941,325 out of 374,424,240
Covered: 31,482,915 out of 374,424,240

Uncovered: 14,984,649 out of 34,124,807
Matches: 12,493,405 out of 34,124,807
Mismatches: 6,245,072 out of 34,124,807
Insertions: 401,681 out of 34,124,807

Populus trichocarpa

Uncovered: 394,207,357 out of 417,137,944
Covered: 22,930,587 out of 417,137,944

Uncovered: 30,653,693 out of 46,257,415
Matches: 10,236,870 out of 46,257,415
Mismatches: 5,037,732 out of 46,257,415
Insertions: 329,120 out of 46,257,415

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)