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cap_final_joined.md

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concatenating all the cap genes predicted and aligned

  • the FINAL one is the one with the predicted complete coding regions.
  • the aligned one is the same aligned for all the indiviual/accessions.

Gaps scores distribution

Number of Residues % Length Cumulative NumberResid. % Cumulative Length Number of Gaps per Column % Gaps per Column Gap Score per Column
5720 98.99619245 5720 98.99619245 0 0 1
1 0.01730702665 5721 99.01349948 1 0.01515151515 0.9848484848
32 0.5538248529 5753 99.56732433 2 0.0303030303 0.9696969697
4 0.06922810661 5757 99.63655244 4 0.06060606061 0.9393939394
1 0.01730702665 5758 99.65385947 9 0.1363636364 0.8636363636
4 0.06922810661 5762 99.72308757 11 0.1666666667 0.8333333333
3 0.05192107996 5765 99.77500865 55 0.8333333333 0.1666666667
8 0.1384562132 5773 99.91346487 61 0.9242424242 0.07575757576
5 0.08653513326 5778 100 65 0.9848484848 0.01515151515
Columns Identity Descriptive Statistics
  • maxColIdentity 1
  • minColIdentity 0.590909
  • avgColIdentity 0.997355
  • stdColIdentity 0.0235959

Description of files:

├── all.cap.gff.clipped.gff: All aligned mRNA positions. ├── capgenes.aligned.fasta.best.anc.dnd: best phylogenetic tree ├── capgenes.aligned.fasta.best.anc.fas: best ancestral sequence ├── capgenes.aligned.fasta.best.dnd: best phylogenetic ancestral tree ├── capgenes.aligned.fasta.best.fas: alignment └── capview.html: visualization of alignment