Abstract: Gobal methane emissions were estimated for 2000–2012 using the CarbonTracker Europe-CH4 (CTE-CH4) data assimilation system. In CTE-CH4, the anthropogenic and biosphere emissions of CH4 are simultaneously constrained by global atmospheric in-situ methane mole fraction observations. We use three configurations developed in Tsuruta et al. (2016) to assess the sensitivity of the CH4 flux estimates to (a) the number of unknown flux scaling factors to be optimized which in turn depends on the choice of underlying land-ecosystem map, and (b) on the parametrization of vertical mixing in the 30 atmospheric transport model TM5. The posterior emission estimates were evaluated by comparing simulations to surface in-situ observation sites, to profile observations made by aircraft, to dry air total column-averaged mole fractions (XCH4) observations from the Total Carbon Column Observing Network (TCCON), and to XCH4 retrievals from the Greenhouse gases Observing SATellite (GOSAT). Our estimated posterior mean global total emissions during 2000–2012 are 516 $\pm$ 51 Tg CH4 yr\textminus1, and emission estimates during 2007–2012 are 18 Tg CH4 yr\textminus1 greater than those from 2001–2006, mainly driven by an 35 increase in emissions from the south America temperate region, the Asia temperate region and Asia tropics. The sensitivity of the flux estimates to the underlying ecosystem map was large for the Asia temperate region and Australia, but not significant in the northern latitude regions, i.e. the north American boreal region, the north American temperate region and Europe. Instead, the posterior estimates for the northern latitude regions show larger sensitivity to the choice of convection scheme in TM5. The Gregory et al. (2000) mixing scheme with faster interhemispheric exchange leads to higher estimated CH4 emissions at northern latitudes, and lower emissions in southern latitudes, compared to the estimates using Tiedtke (1989) convection scheme. Our evaluation with non-assimilated observations showed that posterior mole fractions were better matched with the 5 observations when Gregory et al. (2000) convection scheme was used.