Oryza sativa Japonica vs Brassica rapa LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Brassica rapa (Brassica rapa subsp. pekinensis, IVFCAASv1) 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: 89,504

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

Uncovered: 344,202,788 out of 374,424,240
Covered: 30,221,452 out of 374,424,240

Uncovered: 15,465,464 out of 34,124,807
Matches: 12,078,031 out of 34,124,807
Mismatches: 6,076,580 out of 34,124,807
Insertions: 504,732 out of 34,124,807

Brassica rapa subsp. pekinensis

Uncovered: 263,352,597 out of 283,822,783
Covered: 20,470,186 out of 283,822,783

Uncovered: 33,375,384 out of 48,055,850
Matches: 9,596,582 out of 48,055,850
Mismatches: 4,770,934 out of 48,055,850
Insertions: 312,950 out of 48,055,850

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)