Analysis matrix view
When opening an analysis you are automatically redirected to the analysis matrix view:
The header shows Breed Bio navigation menu icon and the the Genotyper path of your current location.
In the right top corner of this view, action buttons and an analysis summary are shown.
The left panel shows the list of assays (markers) with a search field and buttons to sort the assays either alphabetically 
or by warnings 
.
The center panel summarizes the PCR plate results for each assay.
Tip:
To enable the rich view to and toget a preview of how data is scored per assay and plate. Go to: Settings > General > Summary Settings > Rich view.
Assay and plate statuses
Viewed status
Much like your email inbox, plates that haven't been viewed yet have a thicker line and bold text. When viewing the plate, the line and bold text disappear to mark it as viewed. You can always reset the view status under 'actions' in the top-right corner.
When new data is added to your analysis, the plates and assays are visualized in green. Viewed data has a thick green line on the left which disappears once the plate is viewed.
Tip:
You can always add more read data to your existing analysis to group the data nicely. Use Actions > Add new file(s) or Re-import new data from kraken,
Warnings
Warnings are visualized on both the assay level and PCR plate level. Each assay shows the total amount of warnings of severity high and low available on the PCR plates. Warnings are sorted with the following priority:
PCR plate marked for review by you or a team member (highest priority)
Flagged Assay
Warning severity high, descending number
Warning severity low, descending number (lowest priority)
Plates without warnings 
or with acknowledged warnings 
are ranked alphabetically at the bottom of the assay list.
Navigate to Settings > Manual review to update setting thresholds and severities.
Errors
PCR plate statuses are also visualized in the matrix overview. If a plate has both warning and an error, the error will be visualized prior to the warning.
Failed plate 
Plate not submitted
Plate is excluded from history
Analysis Actions
At the top right corner, you can perform actions from the dropdown menu. All possibilities are explained below.
View used Analysis settings
View which warning settings were set at import time for this analysis.
Drilldown functionality
The drilldown functionality allows users to eliminate bad assay samples originating from the same masterplate (sample plate) well. For example when masterplate well A1 had too little sample volume, you may want to eliminate all samples on the PCR plate related to masterplate A1.
If multiple samples related to the same masterplate well have a bad performance (uncalled or shortfall), the sample is likely to be turned into a bad sample.
The following ratio is used to calculate how samples are drilled down, for datapoints related to the same master plate sample:
# Datapoints for sample with status Called, Failed Control, Passed Control
divided by _______________________________
# Datapoints for sample with status Called, Failed Control, Passed Control, Uncalled, Shortfall
Uncalled means that no call was given and shortfall means that the passive reference fluorescence did not pass the threshold that is set for this instrument (indicative of no mastermix dispension).
All assay samples related to a master plate sample receive the status ‘bad’ in case less than ‘DF’ % of these assay samples received a good call (homozygous, heterozygous or control sample). Bad samples are visualized in a bright yellow color, both on the plate view and in the graph.
For example: 16 datapoints are linked to 1 masterplate sample, of those, 4 are called and the others are uncalled.
Setting the drilldown factor to 25% will set mark all 16 datapoints as 'bad'. Also all other masterplate samples with a drilldown factor <= 25% will be set to bad.
Adding new files
Adding new data to an existing analysis can be performed multiple times as long as the analysis is not authorized. Genotyper searches for differences between the original analysis and newly imported data, and only newly discovered plates, assays and reads (fluorescence) are then added.
The (manual) scores of the original imported data are retained if no new reads are added. New PCR plates or plates to which an extra read is added, are re-analyzed by the algorithm. In this case (manual) scores of the original plate is overwritten.
Only new datapoints (i.e. newly analyzed PCR plate wells) will be added to the usage counter for billing purposes. Datapoints for which a new read is added are not counted towards your usage.
Be aware:
Note that in case of a plate with multiple reads, only the last five reads will be visualised. For example if read 31-35 are shown based on the original imported data and read 36 is added by doing an additional import, the updated analysis will only show read 32-36.
For Kraken users this button is called Re-import new data from Kraken. Re-importing a Kraken order can also be done by manually importing a Kraken analysis that has been imported before. We refer to the Genotyper Drive installation manual for more information about these settings.
Assay results
Click on an assay or plate in the analysis matrix view to go into the the analysis detail view.
On the left panel the assay list is persisten and can be used to navigate assays.
The middle panel shows the plate table and the sample plate view or sample table view.
In the right panel the plot is visualized, used to manually score datapoints.
Tip:
Use left and right arrow keys to navigate between assays.
Use up and down arrow keys to navigate between plates.
Be aware:
When selecting multiple plates, no plates will be shown.
Click on the assayname link above the plate table to be open the assay in the assay configuration view (or CTRL+click to open the assay in a separate tab). Icons next to the assay name give more information about the assay status:
There is a comment regarding this assay in the assay module. Hovering over this icon also shows you the last comment. 
Flagged assay that requires manual review across all analyses or can be set per individual analysis. When sorted on warning message, the flagged assay is shown on top of your analysis matrix overview. 
Some assays are not meant to classify a sample into homozygous or heterozygous genotypes but to check for absence or presence of an allele. This symbol reminds the user this assay is an absence/presence type of assay.
The assay has warnings. Click on this icon to acknowledge the warnings.
Tip:
Use your browser zoom functionality (CTRL + or CTRL -) to scale your Genotyper page.
Plate table and plate actions
The plate table shows sample information for each plate in a row. Hover over the table header to display the settings wheel 
and adjust the table columns to your preferences.
The percentage of all regular datapoints is calculated and sums up to 100%. Shortfall, inconclusive and bad datapoints are only visualized if present on the plate.
Failed controls are visualized as a number compared to the total amount of controls.
The table header shows which warning thresholds are exceeded in the colour of their corresponding severity.
Plate actions for 1 plate can be performed via 
or for a selection of plates via the Actions dropdown menu in the top right corner of the screen. The number of selected plates is shown between brackets.
Following actions can be performed:
Undo user edits for selection: on the selected plates, the edits manually done by any user will be reset.
Include/exclude for history or History inclusion checkbox: the selected plates will not be added to the history grids of their respective assays.
Export selection / Submit selection: default selection.
Export selection as failed / Submit selection as failed
: Upon generating an export file the selected plates will be authorized as failed. A reason for failure needs to be entered. Authorized data will not be added to the history grid.
Failed plates are tracked in Metrics.
Navigate to Settings > General > Failed plate settings to update the reasons for failure.Do not export selection / Do not submit selection
: Upon generating an export file the selected plates will not be submitted back to Kraken and will not be available in the export file. Authorized data will not be added to the history grid. This data will not be saved or tracked in Metrics.Mark selection as (not) viewed or Plate viewed checkbox: A plate is marked as read automatically once you viewed the data. When this happens, the thick line on the left side of the plate table disappears. This is a visual aid to help you organizing which plates are still left for review.
(un)Mark selection for review or Plate marked for review checkbox: Independent whether the data is already viewed, it can be marked for review to make sure you or a colleague knows this plate requires extra attention.
Switch to masterplates or PCR plates or DNA plates: PCR plates are showed by default. Use these actions to switch the view to viewing the data grouped per masterplates or DNA plates (if this information is available in your imported data).
Be aware:
... of the plate and sample selection functionality.
When navigating to an assay, Genotyper will initially select plates as per 'Plate selection behavior' (in Settings -> General): First plate selected or All plates selected.
When manually selecting a plate, Genotyper will select the very same plate during assay navigation. (This behavior can be disabled as per 'Track plates over assays' in Settings -> General).
When manually selecting datapoints, Genotyper will select the plate containing the very same datapoints during assay navigation. If no such plate is found, the default behavior kicks in again.
Plate view
In the plate view, specific PCR (eg. 1536 wells), DNA (eg. 384 wells) and master plates (96 wells) can be viewed and analyzed.
Hovering over a sample will show you the sample information. On top of the plate, following sample selection tools are available:
Switch to sample table view
Sample selection tools (single, column, row, quadrant)
hold CTRL to select multiple samples or drag your cursor over the plate to select a region.Select or deselect all samples at once
Hide or show selected samples
Switch to Passive Reference Dye (PRD) view
Select samples based on master plate
Instrument
Selected datapoints in the graph will be visualized in the plate by means of a grey background color.
The eye-icons 
are available on top of the plate view and in the graph, to hide and unhide selected samples. Note that when multiple plates are selected, the plate view is not shown and so the icons in the graph should be used. Unhiding samples is done with 1 plate selected.
Hidden samples will receive a lighter color in the plate view, both master- and PCR-plate, and will be hidden on the graph. If an outlier is hidden from the plot, the graph will be resized. Hidden samples are not removed from the export file.
Where possible, the sample selection is maintained when you scroll through assays, which makes it possible to easily compare multiple assays for the same sample.
Tip:
Where manual edits were done a pencil icon 
appears. By hovering over the pencil icon the original algorithm score is visualized in the plot view.
Passive Reference Dye view
A passive reference dye (PRD) is used to normalize pipetting variance in your liquid handling equipment. Using a dye that always returns a fluorescence value, we can offset any pipetting variance by normalizing our main fluorescent signals (often, FAM & VIC).
Our passive reference dye view allows you to analyze pipetting artefacts right on the plateview. Click on the PRD icon 
on top of the plate view. Both the plate- and plot-view will change datapoint colors. Switch back via the icon 
.
Higher PRD values appear as dark and larger dots, while lower values appear as lighter and smaller dots. Wells below the instrument's shortfall threshold are clearly marked with a white well and a blue exclamation mark for easy identification.
All PRD values in the plate are ranked from low to high and visualized with a light to dark color. Hover over each well to see the exact fluorescence values (only in the plate view, not in the plot view). Need to see multiple PRD values at once? Open the sample table 
with the icon in the top left corner.
Sample table view
Use the key 
on top of the plate view to switch to sample table view and back.
In the table view, all samples are listed together with other sample info that can be helpful to analyze the results. With the filter, samples can be searched for and grouped.
To select samples, tick of the checkboxes or use CTRL or SHIFT to select multiple datapoints. Your table-settings are saved in your browser session.
Plot view: Assay scoring
On the right panel of the opened analysis view, the plot is visualized with all datapoints of the selected plates.
Upon importing the analysis data is analyzed by the algorithm. The algorithm searches clusters and evaluates the position of each sample and cluster to classify the data.
If available, the algorithm references history grid and control samples for result classification. During this analysis the algorithm classifies the sample into a genotype Y:Y (red), X:Y (green) or X:X (blue) or leaves the sample uncalled (purple).
A fifth class, inconclusive (orange), is available in the plot view. The algorithm will never score a datapoint inconclusive, it can only become inconclusive through manual action. This class is optional to make it possible to distinguish datapoints that were not scored because the algorithm is uncertain (uncalled) from samples that should not be scored (for example samples in the origin: inconclusive).
This extra class can be useful to integrate in your downstream process. Inconclusive samples are added to the history grid.
For polyploid assays, multiple levels are available to score the results.
Adjust the plot view to your preferences by using the tools available in the graph:
move graph area or click on a datapoint to show details
zoom to area or 
or to reset to the original zoom. Zooming can also be done by scrolling scrolling your mouse wheel in a location
resets the graph to the original zoom / pan 
select datapoints by using the lasso tool or the intersection lasso tool
.Datapoints trapped in the lasso can be re-scored with one click. Note that for a group of datapoints only regular datapoints and positive control datapoints are re-scored, but NTC's won't be affected
This way, when a group of samples is rescored or unscored, uncalled NTCs (i.e. NTCs that passed) that lie within a lassoed group will remain passed.
The intersection lasso takes into account which datapoints are already selected on the plate view. Only datapoints that are selected in the plate view, for example 1 quadrant, can be selected on the graph and scored by the intersection lasso. This way, the intersection lasso tool can be used to score a selection of samples related to the same master plate.
History grid is not visualized,
History grid is visualized, 
History is a combination of 2 readers and is not visualized,
History grid is a combination of 2 readers and is visualized (..or use hotkey 'h' to toggle history on/off) 
Show or hide grid lines (.. or use hotkey 'g')
Toggle the graph axis between uniform and fitting around the data (..or use hotkey 'f')
give a call to a selected datapoint(s). If multiple reads are available, the call will be updated for the datapoint in each read.- Show or hide a selection of datapoints
/ 
select to keep samples selected after scoring.
Tip:
use keyboard shortkeys to score a selection of data
1: red (homozygous YY)
2: green (heterozygous)
3: blue (homozygous XX)
4: inconclusive
5: uncalled
A legend for all used colors in the graph is shown in the upper left part of the graph and can be used as a filter.
If data from multiple reads is imported, this is shown with a slider under the graph. Use the slider to scroll over the reads.
Saving behavior of the chosen read depends on your Genotyper settings. See Settings > General > Analysis settings > Read saving behavior and choose from following options:
Manual save only: when selecting a different read than the algo chosen read (for one or multiple plates), this will never be saved automatically. Always use the button
to save your read.Manual save and auto-save upon edits: when selecting a different read than the algo chosen one (for one or multiple plates), this will be be saved automatically after scoring samples on the selected plate(s).
The used read is also listed in the plate table and in the export file. Sample classifications scored by the algorithm or by the user stay the same regardless of the selected read. The user chosen read will be included in the history grid upon authorizing, else the algo chosen read is used.
To authorize the analysis or to perform an action on the analysis, use the breadcrumbs to navigate back to the matrix view.
Exporting & Authorizing
Export
By clicking on Export, a .csv file becomes available to download under Actions > Available download files. This file has the same lay-out for all instrument types and contains datapoint information and genotype classification. Only the last generated export can be downloaded.
For Kraken orders, the export file is created and the data is exported back into Kraken.
Following customizations can be set in Genotyper, to make sure the export fits as good as possible to your lab:
allele labels
If no allele name is available in the input file, by default X and Y will be used in the UI and export file. Simply enter a new allele label and it will be used in all existing analyses as well in future imports and exports.
export mappings
In the assay details tab Export Mappings you can set a mapping for each genotype in the assay, which will be used in the export files.
Especially for heterozygous genotypes this can be useful.
If both an allele Name (set in Assay module) and export mapping are available, the export mapping will have priority to be used in the export file.
Status mappings
Via Settings > UI Status mapping the default status names (uncalled, inconclusive, shortfall, bad) can be renamed.
Export Layout
A series of settings are available in menu Settings > Integrations. Read more about this on our Knowledge page about Settings.
Authorize
Authorize the results to complete and lock the analysis from future editing. By authorizing the analysis, data is added to the history of each assay, unless a PCR plate is manually marked for history exclusion.
Authorizing will create a new export file if applicable. For user of the Genotyper Drive integration with Kraken, the results are exported to Kraken.
Upon authorizing an analysis, a warning message appears allowing the user to:
Exclude all plates from being added to the history grid by ticking off the checkbox ‘disable history generation for this analysis’.
Use this in case of a bigger error in your entire experiment
Disable exporting the results by ticking off the checkbox ‘disable exporting data for this analysis’.
No export file is created and for Kraken users the results are not exported to Kraken.
Be aware:
The history visualization in the analysis plot view, is the history available at authorization time, and is visually saved in the plot view upon authorizing. When looking back at an earlier authorized analysis, a history grid will be visualized representing the history at authorization time.
The history grid used by the algorithm for automated scoring, is updated each time an analysis is authorized. This history grid can be viewed in the assay details page.