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We analysed 866 observations of the neutron star low‐mass X‐ray binary XTE J 1701− 462 during its 2006–2007 outburst. XTE J 1701− 462 is the only example so far of a source that during an outburst showed, beyond any doubt, spectral and timing characteristics both of the Z and atoll type. There are 707  RXTE  observations ( ∼2.5  Ms) of the source in the Z phase and 159 in the atoll phase ( ∼0.5  Ms). We found, respectively, pairs of kilohertz quasi‐periodic oscillations (kHz QPOs) in eight observations during the Z phase and single kHz QPO in six observations during the atoll phase. Using the shift‐and‐add technique, we identified the QPO in the atoll phase as the lower kHz QPO. We found that the lower kHz QPO in the atoll phase has a significantly higher coherence and fractional rms amplitude than any of the kHz QPOs seen during the Z phase, and that in the same frequency range, atoll lower kHz QPOs show coherence and fractional rms amplitude, respectively, two and three times larger than the Z kHz QPOs. Out of the 707 observations in the Z phase, there is no single observation in which the kHz QPOs have a coherence or rms amplitude similar to those seen when XTE J 1701− 462 was in the atoll phase, even though the total exposure time was about five times longer in the Z than in the atoll phase. Since it is observed in the same source, the difference in QPO coherence and rms amplitude between the Z and atoll phase cannot be due to neutron star mass, magnetic field, spin, inclination of the accretion disc, etc. If the QPO frequency is a function of the radius in the accretion disc in which it is produced, our results suggest that in XTE J 1701− 462 the coherence and rms amplitude are not uniquely related to this radius. Here we argue that this difference is instead due to a change in the properties of the accretion flow around the neutron star. Regardless of the precise mechanism, our result shows that effects other than the geometry of space–time around the neutron star have a strong influence on the coherence and rms amplitude of the kHz QPOs, and therefore the coherence and rms amplitude of the kHz QPOs cannot be simply used to deduce the existence of the innermost stable circular orbit around a neutron star.

The kilohertz quasi‐periodic oscillations during the Z and atoll phases of the unique transient XTE J1701−462