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

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?

chloroplast bwa-mem mitochondrial-genome
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updated by Ram Ram • written by kristina.mahan kristina.mahan

1 answer

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

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written by ATpoint ATpoint

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

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written by kristina.mahan kristina.mahan

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

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written by ATpoint ATpoint

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

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written by GenoMax GenoMax

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