I have some RNA-Seq data that I analyzed with tophat2. The command that I used to generate it is
/path/to/tophat-2.1.0/tophat -p 20 -o ouputdir --library-type fr-firststrand /reference/homo_sapiens/GRCh38/ensembl/Sequence/Bowtie2Index/Homo_sapiens.GRC38 my_trimmed_data.fq.gz
This output a file, accepted_hits.bam with 50e6 aligned reads. When I plot histogram of the mapping quality scores, roughly 27e6 reads have a mapping quality value [0-3] and 23e6 reads have a mapping quality value of 50. There are _no_ values in between.
How should I interpret this bimodal distribution of mapping quality scores? This seems very strange to me.