If I have a unique alignment rate of 20%, does that mean my samples are contaminated?

That could be one of the causes, but it could be other issues as well.

An example Sankey Plot of a poor quality sample with 80% unaligned reads.

1. Incorrect species. Aligning your data to the incorrect species is a very common reason for low alignment rates. You should double check that you chose the correct species when uploading your sample. You can do this by clicking into your sample and checking the metadata. Say you wanted to add a mouse sample but selected human as the species, then you would see 95% or more of the reads are unaligned. 

2. Poor sample quality. Low alignment could also be due to poor quality of the samples. Maybe your reads are too short, or they got trimmed really aggressively.

3. Lots of multiply aligned reads. It’s also possible that your sample has a lot of multiply aligned reads. It could be that you have a lot of repetitive regions in your sample, or maybe your read length is really short.

While Basepair provides alignment percentages, interpreting those percentages is up to you as the researcher.