Sanger Trace Chromatogram Viewer
Four-colour AB1 chromatogram rendering with Phred quality scores and reference variant calling.
How it works
Reads the basecalls and the per-base quality record from an .ab1 trace. Quality is expressed on the Phred scale, where Q = −10 × log₁₀(error probability), so Q20 corresponds to 99% base call accuracy and Q30 to 99.9%, and the quality histogram is drawn from the file's own scores. The peak diagram is a schematic drawn from the called bases, NOT the instrument's four fluorescence channels, so it will not show a double peak that the basecaller did not call. Called bases can be compared against a reference to highlight mismatches.
Frequently asked questions
What does a Phred quality score of 30 mean?
Q30 means the probability that the base was called incorrectly is 1 in 1,000, or 99.9% accuracy. The scale is logarithmic: Q20 is 1 error in 100, Q30 is 1 in 1,000, Q40 is 1 in 10,000. Sanger reads typically show low quality in the first 20–40 bases, a high-quality plateau through the middle, and declining quality past 700–900 bases.
Why does my Sanger trace show double peaks?
Overlapping peaks from a certain point onward usually mean more than one template is present — a mixed PCR product, a heterozygous indel, or a pool of edited alleles. A clean trace that becomes doubled at a specific position is the classic signature of a CRISPR-edited population, and the mixture can be deconvoluted to estimate editing efficiency.