I had sequenced a total of 39 microbium samples. Of these 37 are pure cultures, grown in the lab, and the remaining two were randomly obtained from soil.
These samples were sequenced (paired-end sequencing of the 16s metagenome). In case of the pure samples, they all passed the quality checks in FastQC.
However in case of the 2 samples obtained from soil, only the first base of read 1, turned out to be of poor quality. As a result of which, the samples failed the quality check.
Is there any particular reason as to why the first base turned out to be so poor compared to the rest? Does it have any biological significance or is it a library preparation error entirely?