Sanger Chromatogram Viewer
Open .ab1 sequencing files and inspect four-color trace peaks, base calls and quality values in your browser.
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What it does
The Sanger chromatogram viewer opens a raw .ab1 sequencing file and shows you the underlying data behind every base call: the four-color fluorescence traces, the called sequence, and the per-base quality values. It is built for anyone who receives Sanger reads, from molecular biologists checking a cloned insert to technicians verifying a primer or a mutation. Because everything is parsed in your browser, the trace never leaves your computer. There is no upload, no account, and no file size limit beyond what your device can handle, so you can inspect reads on the bench or in the field.
How it works
An .ab1 file stores the raw output of a capillary sequencer. Four dye channels record fluorescence as the fragments pass the detector: the viewer follows the common convention of A in green, C in blue, G in dark, and T in red. Each channel holds a trace, a list of intensity values sampled along the read, and the base caller places a call wherever a channel peaks. Alongside the traces, the file carries a quality value for every base, the Phred-scaled Q score where Q = -10 x log10(error probability); Q20 means a 1 in 100 chance of a wrong call and Q30 a 1 in 1000 chance. Mean signal reports the average intensity of a channel, a quick proxy for how clean the chemistry was.
Worked example
Suppose you open a 900-base read from a plasmid insert. The viewer reports 900 bases, an average quality of 39.2, and 99.1 percent of bases at or above Q20. Scrolling the window to position 410, you see a clean single peak in the green channel (A) sitting well above the other three, confirming the call, while the mean signal per channel reads about 320 to 480 in arbitrary intensity units. Near the 3' end around base 860 the four traces converge and the quality values fall below 20, which is the usual signal to trim before assembling. A heterozygous position would instead show two roughly equal peaks, easily spotted here rather than buried in a plain sequence string.
When to use it
Use the viewer whenever a plain sequence is not enough and you need to see why a base was called. It is the fastest way to confirm a site-directed mutation, to check that a primer sequence matches its trace, or to spot mixed peaks that reveal a heterozygous or contaminated template. Trim low-quality ends before downstream assembly by watching where quality drops below 20. A common pitfall is trusting the called sequence at secondary peaks: when two channels rise together the base caller may emit an N, and you should re-run or re-sequence rather than guess. Another is reading chemistry noise near the start or end as a real variant.
FAQ
- What is an .ab1 file and can I open it here?
- An .ab1 file is the native output of an ABI capillary Sanger sequencer: it contains the four raw fluorescence traces, the called base sequence, and a Phred quality value for every base. This viewer parses the standard ABI/Sanger .ab1 format entirely in your browser, so you can inspect a read without proprietary software. The file is never uploaded, which keeps sequence data private and lets you work offline.
- What do the four trace colors represent?
- Each color is one nucleotide's fluorescence channel. The viewer uses the standard convention of A in green, C in blue, G in dark, and T in red. A base is called wherever one channel rises above the others at a given position, and the colored letters along the trace show those calls. When two channels peak together you are seeing a mixed or heterozygous signal rather than a clean single base.
- What does the Phred quality value mean?
- The quality value Q is a Phred score, Q = -10 x log10(P), where P is the probability the base call is wrong. Q20 means a 1 in 100 error chance and Q30 a 1 in 1000 chance. The viewer reports the average Q across the read and the percentage of bases at or above Q20, a common cutoff for trustworthy sequence. Low Q near the ends is normal and a reason to trim.
- How do I spot a bad or mixed base call?
- Scroll the trace to the position in question and look at the four channels. A confident call shows one clear peak well above the others; a mixed site shows two comparable peaks of different colors, and the caller often reports N there. Very low mean signal, broad overlapping peaks, or a sudden drop in quality all signal unreliable sequence. Such regions should be re-sequenced rather than trusted in an assembly.