Fastqc- Per Base Sequence Quality
There is a pretty good description here. The position in the reads means literally the position in the reads, so position 2 means the quality of all bases on position 2 in the fastq file (all reads). In the description link, you can find how the boxplots and blue and red lines are calculated (and what they mean). They are all based on the total quality values of all bases on a certain position, all bases means all bases of all the reads on a particular position.