This study of achievement differences, as reflected by course grades, on a third-semester electromagnetism course at a Swedish research university was motivated by instructor concerns about gender inequalities. Quantitative analysis showed a gender gap in course grades between female and male students for the period of fall 2007 to spring 2013. Dynamics behind this gap were explored through interpretative discourse analysis on interviews of 21 students who had recently passed the course. A recurring pattern was identified in the interviews. Students described studying electromagnetism as either "studying to pass" or "studying to learn." Their choice of practice was influenced by the significance recognized in the course, which primarily was discussed in relation to program affiliation. Students stressed that perceived differences, in their study context, were larger between students affiliated with different programs than between male and female students on the same program. This was supported by quantitative analysis of course grades in relation to study programs, where the grade difference between female and male students on the same program in most cases were not statistically significant. The gender gap in grades for the whole course was related to different achievements on different programs. Programs further from the discipline of physics had lower mean grades and also enrolled a larger fraction of female students. Society-wide gender differences in interest and study choice are reflected in the grades on this single course. These results displace the achievement gap from the level of individuals to that of programs, and the gender gap from a difference in achievement to a difference in study choice. We discuss the implications of this shift of perspective in relation to gender differences for both research and teaching. [This paper is part of the Focused Collection on Gender in Physics.]