Mapping reads to nuclear, chloroplast, and mitochondria genome separately but all resulting bam files are similar sizes

Question

[kristina.mahan]

I mapped reads onto a nuclear, chloroplast, and mitochondrial genome separately using bwa mem and then sorted using samtools. Entire genome: 179 Mb, chloroplast: 169Kb, mitochondria: 43Kb. The resulting bam files are all similar in sizes (23G, 27G, and 27G). Is their an error? Why would this be the case?

Answer 1

[ATpoint]

Because a BAM contains all reads (mapped and unmapped) that were in the original fastq file, so this is normal and expected.

[kristina.mahan]

so for further process just remove unmapped reads from those bam files?

[ATpoint]

Technically you can do that to reduce file size. If you want that is on you.

[GenoMax]

This would be dependent on aligner options. Some aligners will allow you to drop unmapped reads.