Difference between proper paired reads and mapped and paired reads

Question

[bio_student]

Hi,

I am using samtools stats to get some information about my genome. Can anybody explain to me the difference between reads mapped and paired and reads properly paired?

Thanks.

Answer 1

[Pierre Lindenbaum]

reads mapped and paired

the input of the mapping was a set of two fastq files R1.fq and R2.fq from a paired end experiment

reads properly paired?

reads R1 and R2 from the same segment are mapped on the same chromosome, at a good expected distance with the correct directions. see https://www.slideshare.net/lindenb/ngsformats from slide 30.