Oryza sativa Japonica vs Oryza brachyantha LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) 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: 306,220

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

Uncovered: 227,195,328 out of 374,424,240
Covered: 147,228,912 out of 374,424,240

Uncovered: 2,547,731 out of 34,124,807
Matches: 27,115,006 out of 34,124,807
Mismatches: 3,804,817 out of 34,124,807
Insertions: 657,253 out of 34,124,807

Oryza brachyantha

Uncovered: 150,356,678 out of 260,838,168
Covered: 110,481,490 out of 260,838,168

Uncovered: 4,128,231 out of 33,473,466
Matches: 25,976,721 out of 33,473,466
Mismatches: 2,927,024 out of 33,473,466
Insertions: 441,490 out of 33,473,466

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
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)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Oryza brachyantha
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}