Repeats that affects NIPT results

Question

[khanhlpbao]

I'm working with NIPT project with fastq file extracte from MGI DNB single-end sequencing, despite remove multiple Problematics regions and even Pseudoautosomal on chromosome X and Y. My results have a very high rate of false positive or negative on chromosomes except 13,18 and 21. With chromosomes 13,18 and 21, sometimes the zscore still return false positive or negative. According to some references I found, repeats on genome can cause troubles but I cannot find any articles that can explain for me what kind of repeats and the length of repeats that can cause troubles for sequencing results.