X-ray absorption of $gamma$-ray burst (GRB) afterglows is prevalent yet poorly understood. X-ray derived neutral hydrogen column densities ($N_{rm H}$) of GRB X-ray afterglows show an increase with redshift, which might give a clue for the origin of this absorption. We use more than 350 X-ray afterglows with spectroscopic redshift ($z$) from the Swift XRT repository as well as over 100 Ly,$alpha$ absorption measurements in $z>1.6$ sources. The observed trend of the average optical depth $tau$ at 0.5 keV is consistent with both a sharp increase of host $N_{rm H}(z)$, and an absorbing diffuse intergalactic medium, along with decreasing host contribution to $tau$. We analyze a sub-sample of high-$z$ GRBs with $N_{rm H}$ derived both from the X-ray afterglow and the Ly,$alpha$ line. The increase of X-ray derived $N_{rm H}(z)$ is contrasted by no such increase in the Ly,$alpha$ derived column density. We argue that this discrepancy implies a lack of association between the X-ray and Ly,$alpha$ absorbers at high-$z$. This points towards the X-ray absorption at high $z$ being dominated by an intervening absorber, which lends credibility to an absorbing intergalactic medium contribution.
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