An irregular junction means the 'line' of the cells between the stomach and the esophagus is not cleanly delineated. Could be due to the gastritis seen in the bottom portion of the stomach. With gastritis (acid) that affects the esophagus, changes in the cells are seen and this can result in irregularity.
They will probably look for the presence of H. pylori in the biopsies - a 'typical' culprit in gastritis. They would also look for the presence of any form of cell that should not be found in that organ, or other causes that might result in gastritis.
Cancer isn't a typical cause/result of what they're seeing in this report. It's very likely your doc is going to say you have acid or bile reflux and need to be treated for that.