Theobroma cacao vs Brassica rapa LastZ Results

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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) 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: 191,926

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

Uncovered: 287,522,829 out of 324,719,311
Covered: 37,196,482 out of 324,719,311

Uncovered: 6,400,454 out of 29,183,654
Matches: 15,312,268 out of 29,183,654
Mismatches: 6,742,521 out of 29,183,654
Insertions: 728,411 out of 29,183,654

Brassica rapa

Uncovered: 226,356,511 out of 283,822,783
Covered: 57,466,272 out of 283,822,783

Uncovered: 10,984,493 out of 48,055,850
Matches: 25,570,518 out of 48,055,850
Mismatches: 10,780,856 out of 48,055,850
Insertions: 719,983 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 10,100,000 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}