In a response spectrum analysis, the base shear does not match the summation of shears I get at the base of the columns. Which one should I use as base shear ?
Related query : In a response spectrum analysis, summation of the support reactions does not match the base shear reported. Which one should I use as base shear ?

The one that the software reports as the base shear, is the correct value to use. The column shears ( or support reactions ) reported are all individual maximums and may not occur at the same instant of time. There is a high probability that at the instant when the base shear is maximum, some of the column shears ( or support reactions ) will be less than their individual peak values. Moreover the method used for modal combination, gets rid of signs and hence column shears ( support reactions ) like any other response spectrum output, would be devoid of any sign. Hence one cannot add these up to arrive at the base shear.

There is some useful information on this topic in Section 5.1.10 of this book from the Bentley Press

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