I have around 300 metagenomic sample set of PE-illumina reads. Assembly of these reads give me fairly longer contigs and I can map around 80-90% of my reads back to these contigs.
But when I map same reads to ~5000 complete microbial reference genomes, only a small fraction of reads (2%-8%) are mapped. Even if I forget that I can map my reads back to my contigs, I am surprised to see a metagenomic sample with only 2-8% reads from known microbial genomes.
I have used bowtie2 with default --end-to-end as well as --local settings.
Can any one guess about the probable situation?