Check Complement to display the complement of a sequence alongside. Highlighting can be applied with reference to the consensus or a selected reference sequence.īy default the nucleotide sequence is shown in the sequence view. Go to next disagreement/agreement/transition/transversion/ambiguity goes to the next highlighted feature as described in the previous section on highlighting. When highlighting transitions/transversions, it is recommended you turn on the ignore gaps consensus option or some residues may be wrongly highlighted due the consensus displaying N for sites that contain gaps and non-gaps. Highlight transitions/transversions greys out residues that are not transitions/transversions compared to the consensus sequence. Highlight gaps greys out non-gap positions. Highlight ambiguities greys out non-ambiguous residues. Similarly Highlight agreements greys out residues that are not indentical to the consensus allowing you to quickly locate conserved sites in the alignments. This allows you to quickly locate variable sites in the alignment. When Highlight disagreements is checked, the residues in the alignment that are identical to the consensus state for that column are grayed out. This is particularly useful for exporting sequences to file formats which do not preserve quality (for example FASTA). ![]() Note that if any sequence in the alignment/contig has an internal gap in it, that is still considered valid coverage at that position, and this setting will not apply.Ĭhoose Call N if quality below to change consensus bases to N’s if the quality is below the threshold that you set. If Ref-Seq is selected, then the consensus is assigned whatever character the reference sequence has at that position. ![]() A ‘?’ represents an unknown character, potentially a gap. Options available are -, X/N, ? or Ref-Seq. For example: if there are two G’s and three A’s in a column, with the G’s having qualities of 16 and 24, and the As having qualities of 40, 42, and 50 respectively, then the quality of the consensus will be (40 + 42 + 50) - (16 + 24) = 92.įor alignments or contigs with a reference sequence, the If no coverage call setting can be used to control what character the consensus sequence should use when the reference sequence has no coverage. Select Total to map the sum of the contributing bases, minus the sum of the non-contributing bases. Choose Highest to map the quality of the highest quality base at each column onto the consensus. You can also choose to map the quality of the sequences onto the consensus. This sums the total quality for each potential base call, and if the total for a base exceeds 60% of the total quality for all bases, then that base is called. When the aligned sequences contain quality information in the form of chromatograms, you can select Highest Quality to calculate a majority consensus that takes the relative residue quality into account. When ignore gaps is checked, the consensus is calculated as if each alignment column consisted only of the non-gap characters otherwise, the gap character is treated like a normal residue, but mixing a gap with any other residue in the consensus always produces the total ambiguity symbol (N and X for nucleotides and amino acids, respectively). Hence, an alignment column with only A’s and G’s in equal number will be represented as an R in the consensus sequence regardless of the consensus threshold. In the case of ties, either all or none of the involved residues will be selected. When more than one nucleotide is necessary to reach the desired threshold, this is represented by the best-fit ambiguity symbol in the consensus for protein sequences, this will always be an X. ![]() IUPAC ambiguity codes (such as R for an A or G nucleotide) are counted as fractional support for each nucleotide in the ambiguity set (A and G, in this case), thus two rows with R are counted the same as one row with A and one row with G. A consensus is constructed from the most frequent residues at each site (alignment column), so that the total fraction of rows represented by the selected residues in that column reaches at least a specified threshold. The consensus sequence has the same length (including only untrimmed bases), and shows which residues are conserved (are always the same), and which residues are variable. ![]() When checked, the viewer displays the consensus sequence with the aligned or assembled sequences. These options are available when viewing alignments or contig documents.
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