Thanks @Nicholas_Bokulich - glad to hear I'm not crazy.
I have about 4000 samples that generated some amount of sequence data; these data were generated by pooling between 200-600 sequences per lane (HiSeq or MiSeq). There are 12 lanes of sequencing data in all.
The following visualization should give you a sense of how variable read depth can be per run. All of these data were generated on a MiSeq (HiSeq data still being dedup'd at the moment). What's crazy is the bimodality to a lot of these runs.
