Oryza sativa Japonica vs Theobroma cacao LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Theobroma cacao (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. 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: 146,710

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

Uncovered: 322,458,955 out of 374,424,240
Covered: 51,965,285 out of 374,424,240

Uncovered: 12,926,116 out of 34,124,807
Matches: 13,793,089 out of 34,124,807
Mismatches: 6,937,106 out of 34,124,807
Insertions: 468,496 out of 34,124,807

Theobroma cacao

Uncovered: 321,091,556 out of 345,993,675
Covered: 24,902,119 out of 345,993,675

Uncovered: 19,107,916 out of 34,800,751
Matches: 10,269,229 out of 34,800,751
Mismatches: 5,070,478 out of 34,800,751
Insertions: 353,128 out of 34,800,751

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 Theobroma cacao
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}