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It should be the total number of reads assigned to your list of miRNAs. In a count matrix where columns are samples and rows are genes (or here miRNAs), the total read number per sample would be the column sum.
Mapped reads, because that is what ultimately defines the depth at which a gene or any genomic element has been sequenced. BTW, use TPM instead of RPKM / FPKM, as the latter does not allow to compare between the samples: C: Which normalization method to use FPKM/TPM?