Theobroma cacao vs Brassica rapa LastZ Results

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Theobroma cacao (Theobroma cacao, Theobroma_cacao_20110822) and Brassica rapa (Brassica rapa, Brapa_1.0) 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: 191,843

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

Uncovered: 308,613,188 out of 345,993,675
Covered: 37,380,487 out of 345,993,675

Uncovered: 10,777,157 out of 34,800,751
Matches: 16,085,565 out of 34,800,751
Mismatches: 7,154,703 out of 34,800,751
Insertions: 783,326 out of 34,800,751

Brassica rapa

Uncovered: 226,150,872 out of 283,822,783
Covered: 57,671,911 out of 283,822,783

Uncovered: 10,997,107 out of 48,055,850
Matches: 25,524,308 out of 48,055,850
Mismatches: 10,816,164 out of 48,055,850
Insertions: 718,271 out of 48,055,850

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 rapa
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}