DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

58. Is Q20 a Sufficient Measure of Quality to Use for DNA Sequencing Process Analysis?

D.C. Bruce, M.D. Jones, J.E. Bryant¹, R. Lobb¹, J.R. Griffith¹, M.O. Mundt, N.A. Doggett, and L.L. Deaven

Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 and ¹University of New Mexico, Department of Biochemistry and Molecular Biology, Albuquerque, NM 87131

dbruce@lanl.gov

We examined whether Q20 is a sufficient measure of sequence quality to predict the impact of a process change on the quality of data generated in the shotgun phase. Q20 is a threshold metric derived from DNA sequence trace data by the base-calling program Phred, and is commonly used to report the read length of DNA sequence data. This practice follows from the rubric that 1) the number of Q20 base pairs is a necessary and sufficient quality metric and 2) long Q20 reads improve sequence assembly and hence simplifies finishing. In addition, Q20 is used to perform cost/benefit analysis ($/Q20 base) bearing on sequencing process changes. As a test bed to model a process change, we analyzed data produced from sequencing runs produced with three different sequencing gel formulations. In addition to Q20 statistics, we determined the number of correctly aligned bases and the probability of error at each base for the assembled data. We present data that shows Q20 does not fully predict the benefit or harm associated with process alterations.