Arabidopsis thaliana vs Theobroma cacao LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 119,526

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 82,337,855 out of 119,667,750
Covered: 37,329,895 out of 119,667,750

Uncovered: 7,361,431 out of 33,775,569
Matches: 18,199,825 out of 33,775,569
Mismatches: 7,669,549 out of 33,775,569
Insertions: 544,764 out of 33,775,569

Theobroma cacao

Uncovered: 288,645,961 out of 324,719,311
Covered: 36,073,350 out of 324,719,311

Uncovered: 6,373,474 out of 29,183,654
Matches: 15,529,752 out of 29,183,654
Mismatches: 6,648,202 out of 29,183,654
Insertions: 632,226 out of 29,183,654

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

Arabidopsis thaliana Theobroma cacao
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}