The task Gantt Chart colored portion of the bars reflect the task %Done value (as specified in the drop-down which lists percentages from 0 to 100% in 10% increments), not the Actual % Done value based on actual hours recorded in the timesheets.

Also make sure you are viewing the entire Gantt bar of the task. When the timeline of the Gantt Chart only shows a portion of the task bar, the visual impression of progress on the task is distorted.

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