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For incorporation of unmanned aerial vehicles into the National Airspace, ensuring safety of the airspace including the vehicles, people, and property on the ground is of utmost importance. One of the safety-critical factors for unmanned aviation flights is the risk of deviating from a planned trajectory resulting in a variety of hazards, including potential loss of separation between vehicle and obstacles or unexpected battery energy consumption. Off-nominal conditions introduced by component failures, degraded controllability and environmental disturbances such as wind gusts can lead to unacceptable unexpected deviations from the flight trajectory. It is essential to accurately model such effects on the flight trajectory while computing safety thresholds such as minimum separation from surrounding obstacles, available battery resource to complete the mission or determining delay in the expected time of arrival of flights. In this paper, a tool is presented based on Gaussian Process Regression for wind representation over a pre-defined trajectory for fast, yet approximated, in-time evaluation of possible trajectory deviations caused by wind gusts. The deviation in the planned trajectory caused by wind is further simulated utilizing a 6 degrees-of-freedom (DOF) UAV trajectory simulator comprising of a rotorcraft lumped-mass model with LQRI controller. Both steady-state wind and wind gust effects are investigated. The probability of collision with obstacle is computed and demonstrated on real flight data from experimental flights of an octocopter at NASA Langley Research Center in the presence of simulated obstacles and wind conditions. Effect of varying wind conditions and varying UAV airspeed is further demonstrated on experimental flights in the presence of wind measured by ground based weather service stations. The proposed approach would eventually benefit timely mitigation of current and future safety-critical events in autonomous systems by enabling risk-informed decision making.