Theobroma cacao Belizian Criollo B97-61/B2 vs Camelina sativa LastZ Results

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Theobroma cacao Belizian Criollo B97-61/B2 (Theobroma cacao, Criollo_cocoa_genome_V2) and Camelina sativa (Camelina sativa, Cs) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Theobroma cacao Belizian Criollo B97-61/B2 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: 389,997

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

Uncovered: 274,032,333 out of 324,719,311
Covered: 50,686,978 out of 324,719,311

Uncovered: 5,569,051 out of 29,183,654
Matches: 15,179,155 out of 29,183,654
Mismatches: 7,763,818 out of 29,183,654
Insertions: 671,630 out of 29,183,654

Camelina sativa

Uncovered: 506,952,522 out of 641,356,059
Covered: 134,403,537 out of 641,356,059

Uncovered: 27,529,355 out of 107,028,261
Matches: 54,754,812 out of 107,028,261
Mismatches: 23,087,104 out of 107,028,261
Insertions: 1,656,990 out of 107,028,261

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 Belizian Criollo B97-61/B2 Camelina sativa
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options