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To transition from scoring markers to scoring regions, and for each region and in each sample, we calculated the weighted arithmetic mean for each Sk across the m markers in that region.
Staining intensity and percentage of tumoral cells were taken into consideration for scoring markers.
We assessed the effectiveness of linkage mapping using three types of references for scoring markers: the unmasked genome, repeat masked genome, and gene models.
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Thus, the percentage of all scored markers that identified HF events ranged from 13.2% to 21.6%, with an average of 17.7%, which included all the markers that were monomorphic between the parental lines.
First, the scored markers were roughly classified into seven linkage groups using the color map method.
A chi-squared test was performed to test for 1 1 segregations on all scored markers.
A χ test was performed to test the null hypothesis of 1 1 segregation on all scored markers.
A χ2 test was performed to test the null hypothesis of 1 2 1 segregation on all scored markers.
GBS resulted in a disproportion between the high number of scored markers for the mapping populations and population size.
The number of scored markers is the highest with unmasked scaffolds, moderate with repeat masked scaffolds, and lowest with gene models at 8,501, 4,098, and 776 markers respectively.
The repeat masked genome account for 43% of the assembled genome, but the scored markers are 48% those scored from unmasked genome, for the same reason.
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