Hello @C.F_Zhang,
Welcome to the Qiime 2 forums! :qiime2:
What primers did you use for V3? How long do you expect your amplicon to be?
Here is what I think happened: the miseq correctly sequenced your full region, then it had nothing left to sequence. The 'low quality region' is just noise.
Here is one way you could check this:
vsearch --fastq_mergepairs R1.fastq --reverse R2.fastq \
--fastqout merged.fastq \
--maxdiffs 300 --fastq_allowmergestagger
That crazy high maxdiffs will mean that all reads will join if they can, and allowmergestagger will allows reads to be merged with >100% area of overlap.
I like this idea. If your region is ~120 bp long, this is the perfect choice.
Colin