Newport iServer MicroServer iTHX-M Operator's Manual page 175

color. If the sample does not have an allele call, it is displayed in a
fourth color.
For SNPs on the X chromosome, you may see discrepancies between a
SNP's actual status as called or not called in the SNP table and its
relationship to the displayed model medoids and call zones in the
Scatter Plot for the following reason:
If the sample is not assigned to a gender by the experimenter, SNPs on
the X chromosome are first called using a generic model. The SNP
calls made with this model are evaluated to determine the gender of
the sample, and the SNPs on the X chromosome are then called again
using the appropriate gender-specific model. The calls for X
chromosome SNPs displayed in the Scatter plot are made using the
gender-specific model; however, the generic model medoids and call
zones are displayed in the Scatter Plot.
You can compare SNP allele calls for different samples by comparing
the plot of the RAS values for the samples to the SNP's model medoids
and call zone radii.
Using the SNP Table, you can:
• Select the SNP to be displayed (see
• Highlight a particular sample
You can also print the Scatter Plot
Chapter 5 | Mapping Analysis Window
page 170)
for that SNP (see page 175)
(see page 170).
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