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Quality score filtered marker sets revealed an overrepresentation of type-1 NCO GC (top panel).
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(A2) Varying x between the training and prediction sets revealed several interactions between x and marker density that impacted the accuracy of EBV.
Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker.
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An initial scan of the whole marker set on DNA pools revealed that five markers showed prominent allele frequency difference between the two groups in both populations (Fig. 5).
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The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets.
Linkage and association mapping within our experimental setting reveal significant effects of tightly-linked markers.
Analysis of Spearman correlations revealed that for those individuals that exceeded our arbitrary 0.7 membership threshold group assignment was very consistent across marker sets, with group 1 being the most conserved and well defined.
Expression analysis of a set of muscle growth marker genes revealed clear regulatory roles in relation to swimming-enhanced growth for genes such as growth hormone receptor b (ghrb), insulin-like growth factor 1 receptor a (igf1ra), troponin C (stnnc), slow myosin heavy chain 1 (smyhc1), troponin I2 (tnni2), myosin heavy polypeptide 2 (myhz2) and myostatin (mstnb).
DOI: http://dx.doi.org/10.7554/eLife.01426.012 Repeating the analysis with the filtered set of markers still revealed apparently false positive NCO GC calls.
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