Fig. 6

Circular manhattan plot and qq plot for Grain yield (GY)- a. each of the six experiments (from centre of the plot- 1. lowland non-stress 2014WS (LL_N_WS); 2. lowland non-stress 2015DS (LL_N_DS); 3. lowland stress 2014WS (LL-S_WS); 4. lowland stress 2015DS (LL_S_DS); 5. upland stress 2014WS (UL_S_WS) and 6. upland stress 2015DS (UL_S_DS) for p-values obtained-using Farm-CPU method at two significance thresholds of 1e-4 (blue) and 1e-6 (red). The outermost ring depicts the SNP distribution in the 215,250 SNP working set. Individual experimental results are compared to the combined analysis for each of the three environments- b. LL_N, c. LL_S and d. UL_S, to detect seasonal variation between WS and DS, from centre of the plot-i. WS, ii. DS and iii. Combined analysis