Theobroma cacao vs Brassica napus LastZ Results

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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) 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: 375,370

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

Uncovered: 279,177,925 out of 324,719,311
Covered: 45,541,386 out of 324,719,311

Uncovered: 5,820,270 out of 29,183,654
Matches: 15,114,503 out of 29,183,654
Mismatches: 7,475,390 out of 29,183,654
Insertions: 773,491 out of 29,183,654

Brassica napus

Uncovered: 723,862,666 out of 848,200,303
Covered: 124,337,637 out of 848,200,303

Uncovered: 25,737,667 out of 101,157,402
Matches: 52,150,110 out of 101,157,402
Mismatches: 21,856,546 out of 101,157,402
Insertions: 1,413,079 out of 101,157,402

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 napus
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}