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Hi Everyone:
I had a question regarding the measure, PCT_PF_UQ_READS_ALIGNED, derived by calculatehsmetrics. I know that it is defined as "PF Reads Aligned / PF Reads". For one sample, this turns out to be 0.859744. I have 2960238 PF reads, 30725 unpaired reads, and 77877 unmapped reads, and 1425818 examined read pairs (x2 for reads) were examined.
Adding together examined reads, unmapped reads, and unpaired reads gives me the total number of 2960238. I calculated that the total number of unpaired reads, unmapped reads, and duplicate reads only account for ~4% of the total reads. If ~86% of my reads mapped to the reference and 4% were unmapped, duplicates, or unpaired, what happened to the remaining 10% of my reads?
Thanks!
I had a question regarding the measure, PCT_PF_UQ_READS_ALIGNED, derived by calculatehsmetrics. I know that it is defined as "PF Reads Aligned / PF Reads". For one sample, this turns out to be 0.859744. I have 2960238 PF reads, 30725 unpaired reads, and 77877 unmapped reads, and 1425818 examined read pairs (x2 for reads) were examined.
Adding together examined reads, unmapped reads, and unpaired reads gives me the total number of 2960238. I calculated that the total number of unpaired reads, unmapped reads, and duplicate reads only account for ~4% of the total reads. If ~86% of my reads mapped to the reference and 4% were unmapped, duplicates, or unpaired, what happened to the remaining 10% of my reads?
Thanks!