fastqc report of miseq data
Hi everyone,
I recently got into analyzing 16S rRNA data (miseq). I performed quality check with fastQC and got really bad report. I have attached here for example the per base sequence content. I am very doubtful about getting trustworthy results out of this data. So, I decided to ask the community for suggestions. I would appreciate if anyone could spare some time to have a look on the report and suggest me what should I check to find out reasons for the kind of report and how to fix it.
best regards,
Krishna 
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When you amplify a certain region it is not unexpected to see patterns like this. FastQC is by default set up to look at genome sequence data which is expected to have a more or less uniform distribution of A/G/C/T.
Looks like you have some sort of in-line barcode at the beginning of the read?