Did you set the canvas to be non-premultilied?
gl = someCanvas.getContext("webgl", { premultipliedAlpha: false });
The default for WebGL is true. The default for most OpenGL apps is false
On top of that WebGL is composited with the rest of the page. At a minimum that's the background color of the canvas or whatever it's inside (the body of your document).
To see if this is the problem try setting your canvas's background color to purple or something that will stick out
<canvas ... style="background-color: #F0F;"></canvas>
or in css
canvas { background-color: #F0F; }
OpenGL apps are rarely composited over anything where as WebGL apps effectively are ALWAYS composited.
Some solutions
Turn off alpha
If you don't need alpha in your destination you can turn it off
gl = someCanvas.getContext("webgl", { alpha: false });
Now the alpha will effectively be 1
Set the alpha to 1 at the end of a frame
// clear only the alpha channel to 1
gl.clearColor(1, 1, 1, 1);
gl.colorMask(false, false, false, true);
gl.clear(gl.COLOR_BUFFER_BIT);
don't forget to set the color mask back to all true if you need
to clear the color buffer later
Set the canvas's background color to black
canvas { background-color: #000; }
If possible I'd pick turning off alpha. The reason if is alpha is set to off it's possible the browser can turn off blending when drawing the canvas into the browser. That could be a 10-20% or more increase in speed depending on the GPU. There's no guarantee that any browser makes that optimization, only that it's possible to does whereas with the other 2 solutions it's not possible or at least far less likely
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