Oryza longistaminata vs Oryza sativa Japonica LastZ Results

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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza longistaminata 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: 350,224

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 63,545,502 out of 326,442,508
Covered: 262,897,006 out of 326,442,508

Oryza sativa Japonica Group

Uncovered: 161,634,445 out of 374,424,240
Covered: 212,789,795 out of 374,424,240

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 longistaminata Oryza sativa Japonica
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}