Oryza sativa Japonica vs Arabidopsis lyrata LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) 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: 82,366

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

Uncovered: 345,548,011 out of 374,424,240
Covered: 28,876,229 out of 374,424,240

Uncovered: 16,289,199 out of 34,124,807
Matches: 11,536,344 out of 34,124,807
Mismatches: 5,878,330 out of 34,124,807
Insertions: 420,934 out of 34,124,807

Arabidopsis lyrata subsp. lyrata

Uncovered: 187,824,233 out of 206,667,935
Covered: 18,843,702 out of 206,667,935

Uncovered: 22,202,452 out of 35,389,059
Matches: 8,605,587 out of 35,389,059
Mismatches: 4,312,853 out of 35,389,059
Insertions: 268,167 out of 35,389,059

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)