Is the Bowtie2 "overall alignment rate"...
- The percentage of reads that actually aligned to the reference genome? By that I mean, is this percent the same as saying that "only 75% of the reference genome was covered by your reads?"
- The percentage of fastq data that aligned to the reference genome? So lets say that "100% of the reference genome is covered by the reads, but only 75% of the fastq files were used to cover the reference genome. So the remainder of the fastq data must belong to something else."
I recently purchased a known strain of Candida albicans from a vendor and sequenced its genome using an Illumina MiSeq. I aligned the paired-end fastq files to the strain reference genome and got an overall alignment rate of ~ 43%.
I viewed the BAM results on IGV and from a visual perspective there appeared to heavy coverage across the reference genome, which is why I am questioning the meaning of this "overall alignment rate." Does that mean that 100% of the reference could be covered by the paired-end fastq data and the other ~ 57% could be other DNA? Or does that mean that our sequencing run didn't capture ~57% of the Candida albicans genome?