Oryza sativa Japonica Group vs Theobroma cacao Matina 1-6 LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Theobroma cacao Matina 1-6 (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 125,076

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

Uncovered: 342,335,946 out of 375,049,285
Covered: 32,713,339 out of 375,049,285

Uncovered: 14,196,290 out of 34,424,450
Matches: 13,132,084 out of 34,424,450
Mismatches: 6,646,377 out of 34,424,450
Insertions: 449,699 out of 34,424,450

Theobroma cacao

Uncovered: 317,425,740 out of 345,993,675
Covered: 28,567,935 out of 345,993,675

Uncovered: 14,916,118 out of 34,800,751
Matches: 12,950,388 out of 34,800,751
Mismatches: 6,503,828 out of 34,800,751
Insertions: 430,417 out of 34,800,751

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 Group Theobroma cacao Matina 1-6
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options