I received a BAM of one chromosome and need to determine the percent of the genome covered. Our genome size is 16,600 bp and we did paired-end sequencing each reads being 150 bp long. To my knowledge it should be calculated as follow:

• Genome size : 16,670 bp
• No of base covered: 16,639 bp
• Percent of the genome covered = [(No. of base covered) / (Genome size) ] 100 = (16,639/16,670) 100 = 99.81%

I did the following with samtools depth:

samtools depth -q0 -Q0 my.bam > qry.depth
wc -l qry.depth
16639 qry.depth

Though I don't fully understand the output of samtools depth. To my knowledge the output should be as follow:

• Column 1: ID
• Column 2: Genomic position
• Column 3: No of reads covering that position
• Number of line in qry.depth represents the number of bases covered in the reference

Here is a sample of my qry.depth file:

chrM 1 3
chrM 2 6
chrM 3 16
chrM 4 32
chrM 5 34
chrM 7783 0
chrM 7915 0

The line count of qry.depth is 16,639 but I still have 2 positions with no reads covering them, then what is the percent of the genome covered? Maybe I misunderstood something in the output file format.