I am currently looking through the rep-seqs data from my output after processing paired end reads and I’m noticing that despite running the raw data through DADA2 for ASV clustering, I am getting sequences that are varying in length (which I expected based on the Atacama Soil microbiome tutorial) but some of these ASVs have a 100% ID to each other. For example, the ASVs below both appear to belong to the same taxonomic group, but one is 253 bp and the other is 238 bp. Across it’s 238 bp overlap, they are exactly the same. Is this a result of the parameters i set being too loose or is it possible that they are actually two different populations of organisms? If not, why were they not clustered together?
Thank you for the help!
9c86c998e0d0f9e932e1432be758437b - 238 bp-[ACGCGAGCGTTATCCGGAGTTACTGGGCGTAAAGCGCGTGCAGGCGGACGTGTAAGTCGGTTATGAAATCTCTCGGCTAAACTGGGATAGGTTGACCGAGACTGCCCGTCTAGAGTGAGACAGAGGGACACGGAATTCCGGGTGTAGTGGTGAAATGCGTAGATATCCGGAGGAACACCAGTGGCGAAGGCGGTGTTCTGGGTCTCAACTGACGCTGAGGCGCGAAAGCGTGGGTAGC]
1043bd878aa42f9404e861d36683421f - 253 bp - [AACGTAGGACGCGAGCGTTATCCGGAGTTACTGGGCGTAAAGCGCGTGCAGGCGGACGTGTAAGTCGGTTATGAAATCTCTCGGCTAAACTGGGATAGGTTGACCGAGACTGCCCGTCTAGAGTGAGACAGAGGGACACGGAATTCCGGGTGTAGTGGTGAAATGCGTAGATATCCGGAGGAACACCAGTGGCGAAGGCGGTGTTCTGGGTCTCAACTGACGCTGAGGCGCGAAAGCGTGGGTAGCGAACGGG]