RSEM visualizations in the UCSC Genome Browser. Example visualizations of RSEM output from mouse RNA-Seq data set SRR065546 in the UCSC Genome Browser. (A) Simultaneous visualization of the wiggle output, which gives the expected read depth at each position in the genome, and the BAM output, which gives probabilistically-weighted read alignments. In the BAM track, paired reads are connected by a thin black line and the darkness of the read indicates the posterior probability of its alignment (black meaning high probability). (B) An example gene for which the expected read depth (top track) differs greatly from the read depth computed from uniquely-mapping reads only (bottom track).