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Non-homogeneities in the data were detected using residual analysis as described elsewhere [ 27]. 2 × 2 crossover ANOVA was used for data evaluation.
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For each regression model, autocorrelation of the data was detected using the Durbin-Watson test and corrected using general least squares regression [ 25, 6].
SSRs in the read data were detected using a Perl script in the Simple Sequence Repeat Identification Tool (SSRIT), with minimum thresholds of nine, six, five, five, five, and five repeat units for di-, tetra-,etra-, penta-, hexa-, and heptanucleotide repeats, respectively.
CNVs in the genome data were detected using RDXplorer [ 41] and filtered with a customized pipeline.
The present genes (represented by probe-sets of Affymetrix Gene Chips®) of our microarray data were detected using Affymetrix MAS5 method implemented in Bioconductor packages.
A change in paired data was detected using Wilcoxon matched-pairs signed-rank test.
Myogenic DMRs from the same RRBS data sets were detected using our UPQ algorithm as recently described.
As a result, one locus showing significant imprinting effect was detected in the Imp data (p-value 3.49×10−16) and none were detected using the Dom data, as expected.
For the chloroplast data, two additional reticulation events were detected using PhyML compared to the full-length sequence analysis.
In addition 1547 uaRNA candidates in human were detected using chromatin data.
No significant conversion tracts were detected using GENECONV (data not shown).
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