Theobroma cacao vs Gossypium raimondii LastZ Results

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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Gossypium raimondii (Gossypium raimondii, Graimondii2_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: 308,927

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

Uncovered: 233,209,371 out of 324,719,311
Covered: 91,509,940 out of 324,719,311

Uncovered: 1,480,050 out of 29,183,654
Matches: 22,963,901 out of 29,183,654
Mismatches: 4,312,902 out of 29,183,654
Insertions: 426,801 out of 29,183,654

Gossypium raimondii

Uncovered: 627,092,276 out of 761,405,269
Covered: 134,312,993 out of 761,405,269

Uncovered: 1,523,114 out of 45,523,048
Matches: 36,795,222 out of 45,523,048
Mismatches: 6,736,563 out of 45,523,048
Insertions: 468,149 out of 45,523,048

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 Gossypium raimondii
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}