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The variability of total electron content (TEC) over the crest of equatorial anomaly station Bhopal has been studied during the low solar activity period (2005-2006) using global positioning system (GPS) data. Diurnal variation of TEC is studied for different seasons. Interesting features like the winter anomaly, semiannual anomaly and noon bite out in TEC have been reported. GPS derived TEC is then compared with International Reference Ionosphere (IRI) 2001 model and the difference between predictions and observation is being studied. Using the variability index we have also studied the TEC variability for different seasons and also during quiet and disturbed conditions. A higher variability is observed on quiet days as compared to disturbed days during daytime and nighttime hours.