Theobroma cacao Belizian Criollo B97-61/B2 vs Pistacia vera LastZ Results

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Theobroma cacao Belizian Criollo B97-61/B2 (Theobroma cacao, Criollo_cocoa_genome_V2) and Pistacia vera (Pistacia vera, PisVer_v2) 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: 270,266

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

Uncovered: 264,024,060 out of 324,719,311
Covered: 60,695,251 out of 324,719,311

Uncovered: 2,400,772 out of 29,183,654
Matches: 19,938,712 out of 29,183,654
Mismatches: 6,301,320 out of 29,183,654
Insertions: 542,850 out of 29,183,654

Pistacia vera

Uncovered: 553,681,267 out of 671,152,441
Covered: 117,471,174 out of 671,152,441

Uncovered: 2,740,564 out of 38,113,229
Matches: 26,441,161 out of 38,113,229
Mismatches: 8,352,538 out of 38,113,229
Insertions: 578,966 out of 38,113,229

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 Pistacia vera
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options