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Sequencepage

This is the sequence viewing page, where the primers for your sample have been aligned and are presented for review.

On this page, it is possible to change the base on an automatically determined basecall where the one generated for you is slightly uncertain.

To navigate the sequence, it is possible to use the right and left arrows on the keyboard to scroll between the various bases which were uncertain. If the sequence is clean and contains few mixtures, navigating in this way may bring you directly from the beginning of the sequence to the end of the sequence.

If you would prefer to view all of the bases, including those which were not called with any uncertainty, you can hold down the shift key and navigate using the left and right arrow keys.


Chromatogram Features Edit

Ambiguous BasesEdit

When recall detects a mixture at a certain position that does not have enough clear-cut data to guarantee that it truly is a mixture, it will mark the base as being uncertain. WebRECall does this by surrounding the base call in a yellow square, and it is possible to scroll exclusively between these ambiguous bases while viewing the chromatograms, skipping the intervening distance, by pressing the left and right arrow keys.


Poor-Quality RegionsEdit

Low qual

Primer sequence compromised by dye blob

Occasionally, due to the presence of 'dye-blobs', ethanol or salts picked up in the sequencing process, the quality of sequence produced in certain regions will go down. WebRECall will grey-out regions of particularly poor-quality data, indicating that it has disregarded that section of sequence. An example can be seen where primer 'C' has encountered a blob of dye, causing it to emit bad data. The other primers aligned to that section of sequence are able to provide enough redundant sequence that 'C' is unneeded at this point, however, it is not always possible to cover the complete sequence in this way.

If there is insufficient clean data to cover a poor-quality region, WebRECall will attempt to determine the sequence through the region, however, it is a good idea to patch the region using sequence from another primer.


Page LayoutEdit

Below is located a quick description of all the elements found on the Sample View page.

Job name: This is the name of the sequence collection to which this specific sample belongs. This defaults to the date the collection was uploaded and processed, however, it is possible to rename it on the Start page. The job name will be accompanied by a unique identifier number to distinguish between similarly-named collections and can be found in brackets at the end of this line. ie: (id: 27)
Upload date: This is the date that the collection was uploaded and analyzed.
Mixtures: This is the number of bases which were called as mixtures throughout the sequence. For ease of reference, the percentage area used to determine a mixture is included at the end of the line. ie: (cutoff: 20.0%)
Marks: "Marks" are bases which were ambiguous or difficult to call. These are the ones that are most often reviewed by humans to confirm. If there are too many marks, a sample will be failed.
'N's: Nucleotide which were either found to be uncallable either through poor quality or no-coverage portions of the sequence, or in rare cases, quad-polymorphisms (significant proportions each of C, G, A and T) at that location.
Edited bases: The number of edits made by a human hand.
Errors: Errors which severely affect the viability of the data will be listed here. These errors may include, but are not limited to::*Stop-codons mid-sequence.
  • primers failing to align at all.
  • long stretches of single coverage.
  • Too many 'N' calls.
  • Inserts or deletions which would introduce a frame-shift.
  • Large sections of poor quality sequence.

Chromatogram NavigationEdit

Next marked base: right arrow

Previous marked base: left arrow

Next base: shift + right arrow

Previous base: shift + left arrow

Change base: A,C,G,T,N R,Y,K,M,S,W,B,D,H,V

Erase base: dash

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