Dna Sequences Base Calling by Phred: Error Pattern Analysis

PHRED is the most frequently used base caller algorithm in genome projects. An interesting point on PHRED utilization is the fact that a low score on some base may not actually correspond to a miscalling on that base, but it may stand for a putative error on the region around this base. In order to evaluate the efficiency of PHRED on base calling and base quality assigning, we have sequenced pUC18 and compared sequences called by PHRED with pUC18 published sequence using Smith-Waterman algorithm. Our results depict a detailed pattern of errors incorporated by the algorithm, confirm that PHRED provides appropriated base calling but: low-quality regions have their quality usually under-estimated, with most errors being mismatches. On the other side, high-quality regions have super-estimated quality, with errors mainly represented by deletions.