Oryza sativa Japonica Group vs Theobroma cacao Belizian Criollo B97-61/B2 LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Theobroma cacao Belizian Criollo B97-61/B2 (Theobroma cacao, Criollo_cocoa_genome_V2) 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.


Number of alignment blocks: 125,045

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

Uncovered: 342,635,399 out of 375,049,285
Covered: 32,413,886 out of 375,049,285

Uncovered: 14,152,070 out of 34,349,962
Matches: 13,135,145 out of 34,349,962
Mismatches: 6,614,863 out of 34,349,962
Insertions: 447,884 out of 34,349,962

Theobroma cacao

Uncovered: 296,301,792 out of 324,719,311
Covered: 28,417,519 out of 324,719,311

Uncovered: 10,230,110 out of 29,183,654
Matches: 12,376,191 out of 29,183,654
Mismatches: 6,178,015 out of 29,183,654
Insertions: 399,338 out of 29,183,654

Configuration parameters

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)
     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 Belizian Criollo B97-61/B2
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}