I have used bwa mem 0.7.12 to map PacBio reads on a reference genome. Then I want to have some statistics on this mapping. When I count the total number of reads in the starting fastq file, the result is 250,000) I have used my favorite tool : Qualimap2.2 But in the result the number of total reads and mapped reads are abnormaly high : resp 612,000/598,000 I have tried also with samtools 1.3 (samtools flagstat). But the result is the same : the number of total reads and mapped reads are abnormaly high : resp 612,000/598,000
How explain this huge difference ?
Am I doing something wrong ?
Thanks for your help and expertise