Hi, so how should we count for mapping rates for ChIP-seq? I used "samtools flagstat", but it always showed 100% mapping. For example, I have a fastq file, there are 136,192,060 lines in the file, so there should be 136,192,060/4=34,048,015 reads in this file. After mapping the reads to reference genome, Iused 'samtools flagstat' to see the mapping rate, it showed "11,892,792 + 0 mapped (100.00% : N/A)". But the mapped reads(11,892,792) is far lower than the original reads(34,048,015), how could the mapping rate be 100%? Thanks! And also, after trim-galore, the QC result showed the total sequences of the file is 9,477,948. So actually where does this number come from? Thanks so much!