Displaying Data

# Displaying Data |  | Back | Contents | Next |
| ## Base calls Base calls can be hidden or displayed above the peaks by clicking the Base Calls button in the toolbar or selecting View > Base Calls from the menu. When a base is clicked in the trace window, the base call is also displayed in the status bar in the lower left of the main FinchTV window along with its base position and quality value (if present). ## Base Positions Base position numbers can be hidden or displayed by clicking the Base Position Numbers button in the toolbar or selecting View > Base Position Numbers. ## Quality values Some chromatogram files contain quality information about the base calls (the quality values may be from the KB basecaller, Phred, or TraceTuner, depending on the chromatogram). If quality information is present in the chromatogram, it can be displayed in FinchTV. If this information is not available, that option is disabled. The quality values can be displayed or hidden by clicking the Quality Values button in the toolbar or selecting View > Quality Values from the menu. An aqua-colored horizontal line is placed across the quality bars at Q=20. Bars above this line indicate base calls that have a better than 99% probability of being correct. Those below have less than a 99% probability of being correct. When a base is clicked, the quality value is also displayed in the status bar in the lower left of the main FinchTV window. ## Reverse complementing the trace and sequence In FinchTV 1.3, and above, the trace, and its corresponding sequence, can be reverse complemented. The reverse complement can be displayed by clicking the Reverse Complement button in the toolbar or selecting View > Reverse Complement from the menu. Bases are numbered left to right in ascending order regardless of trace orientation. ## Displaying the raw trace data ABI formatted chromatogram files also contain raw, pre-processed, trace data. Displaying this information can be useful for troubleshooting sequencing instruments. In FinchTV 1.3, raw trace data can be displayed by selecting View > Raw Data from the menu. This will pop up a new window displaying the data. The scaling and window controls on the Raw Data Window operate similar to those of in the Standard View. ## The Raw Data Window always displays raw trace data in the "forward" orientation, even if the main window is displaying the reverse complemented trace and sequence. ## Chromatogram information Other information contained in the chromatogram file can be displayed by clicking the Chromatogram Info button in the toolbar, selecting View > Chromatogram Info from the menu, or typing cmd I (Mac) or ctrl I (others). The FASTA sequence is shown in the first tab in Chromatogram Info: Sequence. Additional information about the chromatogram can be viewed by clicking on the second and third tabs. |  |
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