Sequencing Coverage difference after alignment?

[AlexanderM-M]

Hey guys,

I have a ˜20x Data set of human brain genome and aligned it first with ngmlr and then with minimap2 (I used the fastq).

After aligning I checked the coverage and saw this:

samtools depth fastq_pass/all_reads_ngmlr.sorted.bam | awk '{sum +=$3; n++} END {if(n>0) print sum / n;}'
3.14177

samtools depth fastq_pass/all_reads_minimap2.sorted.bam | awk '{sum +=$3; n++} END {if(n>0) print sum / n;}'
23.8959

I don't know how to explain this difference? Do you maybe have an idea?

All the best and thanks in advance for your answer!