The
Linkage Group and Segregation
tab is shown below:
The
Linkage Group and Segregation
tab contains the following elements:
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This plot shows a point for each marker in the analysis. The
-log
10
transformed
p
-value for the
chi-square
test (optionally adjusted for multiple testing) for segregation distortion is on the
y
-axis. The
x
-axis shows the difference in the percentage of
alleles
from parental line 1 (denoted as the "A" allele) less the percentage of alleles from parental line 2 (the "B" allele). Markers that are in the upper left or right corners are those that can exhibit unexpected ratios of alleles based on the inbred cross specified on the
dialog
.
For example, with the
BC1_example
setting, the experimental
population
is from a backcross to parental line 1 ("A" allele), so we expect to see frequency ratios of 50% of AA
homozygous
genotypes
to 50% AB
heterozygous
genotypes. The expected segregation ratios are assumed based on the cross for Backcross, F2, RIL, and DH cross types. This can be customized to test user-supplied expected ratios on the dialog with the Expected Segregation Ratios for AA AB BB parameter.
The markers in this plot are colored by
linkage
group membership (value of LGroup
variable
). If a framework map was specified, markers belonging to an original framework group will be denoted with a star marker.
Note
: Any markers lying above the red dotted line should be considered in segregation distortion based on the tested allele frequency ratios
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One or more linkage group
distribution
analyses
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The results shown on this tab are interactive and linked to those shown on the
Linkage Group Results
tab. You can select marker(s) in the segregation test plot or groups of markers by clicking on the histograms in the distribution analyses. You can then see where these markers lie in the linkage group results on the first tab or choose to exclude selected markers with the
Exclude Markers and Rerun Analysis
action button.