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The 234 distorted markers were excluded from the linkage analysis because they could lead to false linkage between some markers or linkage groups.
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This was done to avoid false linkages from the expected Mendelian segregation ratio.
False linkages would likely have dissimilar injury characteristics, artificially lowering coding agreement.
628 records had differing CHI numbers, and are therefore potential false linkages from our type of probability linkage.
As many turning points and false linkages were considered, these contigs were manually assembled by the following criteria.
These were excluded from further analyses due to their tendency to introduce false linkages into the analysis.
The high quality marker data helped in generation of marker linkage groups without obvious inflation of map distances that can be caused by false linkages [ 45].
Independent markers showing significant segregation distortion and markers with missing data (> 10%) were rejected for linkage to avoid bias and false linkages.
Overall, errors in identifying parnered and unique k-mers should shorten contigs and scaffolds and hide linkage, not promote false linkages.
Markers that were distorted significantly with P < 0.0001 were not considered because ratios that are too skewed might create inaccurate distances and false linkages (Cervera et al. 2001).
Because a large number of loci were included in this analysis, moderately distorted loci (0.001 < P < 0.01) were retained but kept under observation in the event that they became implicated in false linkages at a later stage.
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