Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer User Manual page 116

8
Chapter 8 View and analyze results
View results on the instrument
Result
CRL (Contiguous Read
Length)
Exported
Well details
Sample file name, QC flag, sample name, CRL, signal strength, Median PUP, Trace score, run module and dye set
used to acquire the data, and export status.
Signal strength
Trace score
Median PUP (pull-up peak)
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The longest uninterrupted segment of bases with an average Quality Value (QV) ³20.
In addition to evaluating the QV of a base call, the software considers the QV of adjacent
bases within a ±21-bp moving average to determine a contiguous read length based on
quality values.
Note: The contiguous read length passing criteria for install checks is an
uninterrupted segment of bases with an average Quality Value (QV) of 30.
The sample has been auto exported (saved to the Connect cloud-based platform,
network, or USB) or manually exported (using
name 4Export).
Well details (see below).
The average relative fluorescence unit (RFU) for all dyes across the electropherogram
in the raw data.
The average basecall Quality Value (QV) of bases in the clear range sequence of a trace.
clear range is the region of the sequence that remains after excluding the low-
The
quality or error-prone sequence at the 5¢ and 3¢ ends. The clear range is calculated by
the KB basecaller using QVs.
A measure of noise or pull-up that is determined by taking the mean of the ratios of
signal strength calculated for each base-called peak: primary peak/secondary peak
under the primary peak.
A higher value indicates less baseline or secondary noise. A lower value indicates an
elevated baseline or secondary noise.
Example 1: Main called base signal strength is 1,000 RFU and the largest secondary
peak beneath it is 10 RFU; PuP=100
Example 2: Main called base signal strength is 1,000 RFU and the largest secondary
peak beneath it is 100 RFU; PuP=10
Understanding Quality Values (QVs)
Quality value ranges
The color of a QV bar indicates the QV of a base.
• Pure base with QV ³20
• Pure base with QV 15–19
• Pure base with QV <15
• Mixed base
Description
Settings4Run History4
SeqStudio Genetic Analyzer Instrument and Software User Guide
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