I am determining the number of copies of rDNAs (RNA45SN2 gene) using WGS sequencing (Illumina) and hg38 as a reference genome. While rDNA sequences are present on human chromosomes 13, 14, 15, 21 and 22 (consisting of multiple 45S rDNA repeat units that vary in number among individuals and chromosomes) in hg38 rDNA only two reference copies are presented on chromosome 21. To calculate the copy numbers I use CNVkit, where copy numbers (in the first approximation) are calculated based on the proportion of the reads supporting the target position to the average genome coverage.
My question is, will my reads align equally within both copies of the reference rDNA sequences on hg38? Should I, therefore, count CNV per sequenced sample as a sum of CNV coming from both sites or only one of them?