Theobroma cacao vs Arabidopsis lyrata LastZ Results

Back to all analyses

Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.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: 132,859

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

Uncovered: 287,770,419 out of 324,719,311
Covered: 36,948,892 out of 324,719,311

Uncovered: 6,211,966 out of 29,183,654
Matches: 15,603,304 out of 29,183,654
Mismatches: 6,729,971 out of 29,183,654
Insertions: 638,413 out of 29,183,654

Arabidopsis lyrata subsp. lyrata

Uncovered: 165,069,572 out of 206,667,935
Covered: 41,598,363 out of 206,667,935

Uncovered: 8,344,759 out of 35,389,059
Matches: 18,673,797 out of 35,389,059
Mismatches: 7,832,015 out of 35,389,059
Insertions: 538,488 out of 35,389,059

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 Arabidopsis lyrata
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}