Need explain about number of mapped reads and total number reads

Question

[khanhlpbao]

Hi, I'm studying the article about NIFTY test as literature review (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544640/). And I have some problems that I cannot understood. Its about the fomular of kmer coverage, the k-mer coverage for each chromosome is calculate as (number of unique reads mapped onto chromosome)/(total number of unique reads for chromosome). I don't know what is unique reads mapped onto chromosome and how to calculate it by using samtools. Because every answer always lead to my kmer coverage is 1 on all samples I found with different %GC. Thank you very much

[Istvan Albert]

(number of unique reads mapped onto chromosome)/(total number of unique reads for chromosome)

this definition does not seem to make much sense. First reads are not kmers, thus it not clear how the above could give you anything related to kmers.

then it is not clear what the words even mean, the definitions for the numerator and denominator appear to be the same,

specifically what would be the difference between "number" and "total number"? In what way is the first number not a "total"?