Oryza sativa Japonica vs Dioscorea rotundata LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Dioscorea rotundata (Dioscorea rotundata, TDr96_F1_Pseudo_Chromosome_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 143,155

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

Uncovered: 336,707,692 out of 375,049,285
Covered: 38,341,593 out of 375,049,285

Uncovered: 12,491,574 out of 34,403,043
Matches: 14,227,497 out of 34,403,043
Mismatches: 7,108,123 out of 34,403,043
Insertions: 575,849 out of 34,403,043

Dioscorea rotundata

Uncovered: 420,726,517 out of 456,674,974
Covered: 35,948,457 out of 456,674,974

Uncovered: 7,368,413 out of 24,441,241
Matches: 11,385,171 out of 24,441,241
Mismatches: 5,309,604 out of 24,441,241
Insertions: 378,053 out of 24,441,241

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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 Dioscorea rotundata
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}