Theobroma cacao vs Brassica oleracea LastZ Results

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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Theobroma cacao 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: 214,630

Genome coverage (bp) Coding exon coverage (bp)
Theobroma cacao

Uncovered: 286,289,457 out of 324,719,311
Covered: 38,429,854 out of 324,719,311

Uncovered: 6,292,223 out of 29,183,654
Matches: 15,343,321 out of 29,183,654
Mismatches: 6,810,369 out of 29,183,654
Insertions: 737,741 out of 29,183,654

Brassica oleracea var. oleracea

Uncovered: 424,235,516 out of 488,622,507
Covered: 64,386,991 out of 488,622,507

Uncovered: 21,199,152 out of 61,722,508
Matches: 27,853,660 out of 61,722,508
Mismatches: 11,861,488 out of 61,722,508
Insertions: 808,208 out of 61,722,508

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

Theobroma cacao Brassica oleracea
Chunk size 10,100,000 10,100,000
Overlap 100,000 100,000
Group set size 10,100,000 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}