Interpreting DNA sequencing data: what can you get from quality scores?

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Sandra Porter
Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform. Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data analyst or bioinformatics technician does in a DNA diagnostics company. As you might imagine, looking at every single DNA sample by eye gets rather tiring. One of the things that informatics companies (like ours) do, is to try and help people analyze several samples at once so that they can scan fewer individual samples. You might be wondering how we do that. One of the things we do is to give people tools that let them scan several samples at once. The examples below show quality plots for reads. Every quality value for every base in a read is plotted on the y axis and the position within the sequence, on the x axis.
Question: Which read(s):
  • 1. contains either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base?
  • 2. doesn't have any DNA?
  • 3. is a PCR product?
More than one answer might be correct.

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