As has been indicated, source magnitudes and positions are derived independently in each color band. The detections in each band are merged into a single source listing using the positions and uncertainties in each band. The merging algorithm is based on positional proximity, but contains hierarchical logic to rectify confused matches (i.e. when there is more than one possible match between bands). Updated positions are derived from signal-to-noise weighted averages from the bands in which there are detections, and in which the information in the contributing band is not considered to be confused. Sources which have possible confusion in the bandmerge process are indicated by the Confusion and Contamination flag in the Point Source Catalog record ("cc_flg" = "B").
When a merged source does not have a measurement in a given band, a band-fill is made by measuring the flux and noise in a 10" radius aperture at the source position on the Atlas Images of the undetected bands. The 2MASS Source Catalogs contain a 95% confidence upper limit for non-detected bands in the "default magnitude" fields, that is based on the measurement and uncertainty in the aperture, and the local noise in the image. The actual measured magnitude and error are also quoted for non-detected bands in the "standard aperture" magnitude fields so users may apply their favorite algorithm for evaluating upper limits. Note that negative flux aperture measurements are specially encoded since the brightness fields are listed as magnitudes.