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Haplotypes in adjacent marker windows are aligned using a heterozygote near the middle of the overlap.
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Decreased accuracy near the edge of the marker windows is avoided by using overlapping windows and trimming half of the overlap from each window prior to merging data in adjacent windows.
By default a 10-marker window was used to estimate the IBD probabilities.
As the STLDLA and STLD QTL peaks for CM were in a narrow region, a four-marker window was used to estimate the IBD probabilities.
A five marker sliding window was then moved across the two proximal bins in a forward and reverse direction and a genotype call was obtained at each point.
A 10 cM blockout window (any markers in that window are blocked) on each side of the test position was used to exclude nearby background markers from being covariates in the regression model.
An inherent assumption of these methods is that the individual marker estimates within a window are independently and identically distributed.
Cafeteria windows were tagged with black marker with the phrases "F*** School" and "Sincerely Class of 2012," Kravetz said.
Windows were removed that contained >50% ' N' in the sequence assembly, as were windows at the beginning, end and centromere of chromosomes with no markers detected in them.
A maximum of five significant markers outside of the test window, were selected as background controls and fitted to a forward and reverse regression models as coefficients to control for genetic variation (13).
The average marker density (i.e. average distance in kb between two adjacent markers) was equal to 61.0 kb, ranging from 54.6 to 70.9 kb, and the average r 2 between adjacent markers within each 1 Mb window was 0.237, ranging from 0.192 to 0.269.
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