Hi, I use MosaikAligner to map pair-end reads to the genome(know the genome_size). I get the bam format file(a.bam). a.bam have all the mapped results including the unmapped,the mapped (unique-anlignmed and multiply-aligned) reads. I want to get the coverage and coverage rate of a.bam. I use 2 ways:

First way:

because the size of a.bam is too huge, I want to reduce the size. So
I use samtools -F 8 to get mapped reads file.

 - samtools view -b -F 8 a.bam > a.map.bam
 - samtools sort a.map.bam a.map.sort
 - samtools depth a.map.sort.bam | awk '{if ($3 > 0){n++;sum+=$3}} END {print "The coverage rate =", n/genome_size,"\t", "The coverage depth =", sum/genome_size}

The result: The coverage rate =0.58 the coverage depth = 12X

Second way:

 I do not reduce the unmapped reads.

- samtools sort a.bam a.sort
- samtools depth a.sort.bam | awk '{if ($3 > 0){n++;sum+=$3}} END {print "The coverage rate =", n/genome_size,"\t", "The coverage depth =", sum/genome_size}

The result: The coverage rate =0.59the coverage depth = 13X

• However, why do the second way that I get bigger coverage rate and coverage depth than the first way ? And why do the unmapped reads can contribute to the increase of the coverage rate and depth ? More importantly, I want to know which way is right.