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As mentioned in the paper, there are three reasons: (1)2 Convolutional layers allow CAECseq to capture spatial relationships (correlations) between SNPs. Therefore, random shufflingdestroyedthespatial relationship between SNPs thattheconvolutional layers originally19 captured. Q8: An empty cell in the example read in Figure 1 is confusing. The empty space models gaps in coverage of30 paired-end reads. Thisshouldbeexplained[...] AciteshouldbegivenforPReLU.38 Thanks, we are committed to making these updates!