Emissions are aggregated by flight segment (LTO, wheels-up to wheels-down, stratospheric, etc.). They are aggregated at a higher level by aircraft type or ICAO-24 bit identifier, by city pairs, by airport of departure, etc. 

The chemical species that are calculated are: CO2, CO, NOx, SOx, UHC, H2O, soot, nvPM (non-volatile Particulate Matter), VOC (volatile organic compounds), dust concentration and dosage (if data are available).

An example of emissions aggregations in shown in the graph below, where we display the predicted emissions of nvPM, as distributed vertically in 1,000 feet bins, for an Airbus A330-343 (Rolls-Royce Trent 700 engines). 

You may be interested in this additional note for further information.

Or you can read one of our papers on this matter.