In the following MWE, I used \widthof from the calc package in order to measure the width of the entry in the \multicolumn command. I then used 6 wc type columns from the array package instead of the regular c type columns. I then made sure, to use half of the before determined width as the width argument of the wc column.

The table in the following MWE exceeds the textwidth. I decided to not address that issue, since there was no documentclass given in the original question and I just guessed one.
\documentclass{article}
\usepackage[table]{xcolor}
\usepackage{array} % for the w column type
\usepackage{calc} % for the \widthof command
\newlength{\mycolwidth}
\setlength{\mycolwidth}{\widthof{CoreExome-24 v1.0}}
\begin{document}
\begin{table}
\centering
\rowcolors{1}{}{lightgray}
\begin{tabular}{|l|*{6}{wc{0.5\mycolwidth-2\tabcolsep}|}}
\hline
\multicolumn{7}{|c|}{Sample QC} \
\hline
\multicolumn{1}{|c|}{} & \multicolumn{2}{c|}{CoreExome-24 v1.0} & \multicolumn{2}{c|}{CoreExome-24 v1.0} & \multicolumn{2}{c|}{CoreExome-24 v1.1}\
\cline{2-7}
\multicolumn{1}{|c|}{QC Flag} & # & % & # & % & # & % \
\hline
UNUSUAL_XY & 19 & 0.09 & 70 & 0.18 & 70 & 0.18 \
\hline
\end{tabular}
\end{table}
\end{document}