Story goes like this -- if internal contamination is larger in the low-biomass inoculum samples, then these samples will tend towards the plate mean (or the means of their respective rows/cols if index hopping is the main issue). A simple first check is to see whether the number and/or proportion of reads from positive control taxa (T. mobilis; Zymo (A1 only)) are associated with the sample's biomass (as measured DNA concentration).
Story goes like this -- if internal contamination is larger in the low-biomass inoculum samples, then these samples will tend towards the plate mean (or the means of their respective rows/cols if index hopping is the main issue). A simple first check is to see whether the number and/or proportion of reads from positive control taxa (T. mobilis; Zymo (A1 only)) are associated with the sample's biomass (as measured DNA concentration).