To assess the conformity of marker segregation with that expected from the population type, QGene computes the chi-square goodness-of-fit statistic and plots the genotype frequencies at all loci. As with the Single-marker and Interval plots, you can scroll the contour horizontally by clicking in the scroll bar, using the arrow keys, or dragging with the mouse past the edge of the contour window. In the histograms, the segregation proportion of each genotype class is plotted for all the markers; in the figure it can be seen that their means are in near the 1:1 ratio expected for an inbred progeny, with a small proportion of heterozygous individuals corresponding to the incompletely inbred F7 population used for this example. The vertical bars in the histograms represent the positions of the classes for the current locus (Xbcd1380a in the figure).
The dialog also gives the total marker-allele counts in the population, under Totals, and shows the distribution of missing-marker data by locus. The bimodal distribution in the "-" (missing-data) histogram below arises from most of the marker loci giving 0 to 10% missing data, while a group of them that were assayed on only half of the population are missing 50% of genotype data.
We can also examine the distribution of genotype-segment lengths at each marker in the map, when the By segment button is clicked.
QGene has classified by length and marker genotype, for each marker in turn, every continuous map segment on which that marker lies. The vertical height of each point on a contour corresponds to the mean length of segments containing the corresponding locus and having the genotype whose color code corresponds to that contour. Not surprisingly, segments are shorter at the ends of chromosomes.
There has been considerable discussion in the literature about the changing mean lengths of genome segments with generation advance; this plot gives a graphic rendering of the phenomenon.
In this analysis QGene tabulates by marker genotype and length, and shows in histograms, the distribution of map lengths of chromosomal segments in the population. The length of a segment around any marker is calculated as the sum in cM of the half-intervals on either side, or, if the marker is terminal on its chromosome, just the proximal half-interval. The possible genotypes of a segment are thus either parental homozygote, heterozygote (with linkage phase ignored), dominant with ambiguous genotype, and missing.
The histograms are all on the same vertical scale. The number at top left of each shows the size of the largest class. Clicking in a histogram opens an edit/export dialog for it.
If the By individual button is clicked, QGene computes the proportion of the part of each individual's genome accounted for by segments of each genotype (or missing genotype) and shows these proportions as population distributions in uniplots. The proportion of total genome length made up by missing data is also shown. The contours in the box at bottom represent the proportions for each individual; to find an individual and see these statistics, drag in this contour box, click in the list of names, or type the individual's name in the edit box. To sort the population on proportion of a selected marker genotype, Command-click in the uniplot of that genotype. To save into the Transformed trait, for other kinds of analysis, the genome proportions for the current genotype, use the Save as trait button.
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