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Genotyping quality was high, with all duplicated samples showing perfect concordance.
The total genotype mismatch rate was 0.73% for duplicated SNPs and 0.76% for duplicated samples.
One major drawback associated with over-sampling is that learning on duplicated samples can lead to overfitting [ 14].
RNA-seq libraries were generated from duplicated samples per condition using the Next Illumina Ultra RNA library prep kit (NEB) following manufacturer's protocols.
Results confirmed the data homogeneity (data not shown) and then we merge the data of duplicated samples.
Blinded duplicated samples indicated no genotyping error.
The duplicated samples showed 99.9% concordance of genotypes calls.
Another limitation of this study is the small number of duplicated samples.
Sample sets were checked for genetic outliers and duplicated samples, which were removed.
Given the problem of sample mislabeling, several preliminary analyses to identify duplicated samples and preliminary runs with Structure were performed to exclude offtypes and human mediated hybrids.
The genotyping error rate per locus has been calculated as the ratio between the observed number of differences and the total number of comparisons across the duplicated samples [29].
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