Strain Fitness in Pseudomonas putida KT2440 around PP_3008

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs

Only strains with sufficient reads to estimate fitness are shown, but the strain fitness values are still rather noisy and may be biased towards zero. Strains near the edge of a gene are not shown as being associated with that gene (they are in grey). Strains in the central 10-90% of a gene are color coded by the insertion's strand. Usually, "+" means that the selectable marker is encoded on the forward strand, i.e., transcribed rightward.

Per-strain Table

Position	Strand	Gene	LocusTag	Fraction	Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=sterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=144_hrs
3,400,485	-		PP_3006	0.85	-0.6
3,400,526	-				-1.9
3,400,590	-				+0.3
3,400,590	-				-1.7
3,400,636	+				+0.2
3,400,636	+				+0.0
3,400,657	+				-1.2
3,400,658	-				-1.4
3,400,658	-				-0.8
3,400,695	+				-1.2
3,400,696	-				+1.3
3,400,696	-				-0.8
3,400,696	-				-2.0
3,400,696	-				+0.2
3,400,696	-				+0.5
3,400,696	-				+0.5
3,400,696	-				+1.7
3,400,696	-				+0.3
3,400,707	+				-0.7
3,400,794	+		PP_3007	0.23	+0.4
3,400,794	+		PP_3007	0.23	-0.3
3,400,794	+		PP_3007	0.23	+1.4
3,400,795	-				-1.6
3,400,795	-		PP_3007	0.23	-1.0
3,400,795	-		PP_3007	0.23	+0.6
3,400,795	-		PP_3007	0.23	+0.6
3,400,795	-		PP_3007	0.23	+1.7
3,400,795	-		PP_3007	0.23	-0.7
3,400,930	+		PP_3007	0.49	-1.4
3,400,948	-		PP_3007	0.52	+1.1
3,400,948	-		PP_3007	0.52	+1.3
3,401,049	+		PP_3007	0.71	-2.3
3,401,049	+		PP_3007	0.71	-1.8
3,401,049	+		PP_3007	0.71	-1.6
3,401,050	-		PP_3007	0.71	-0.8
3,401,050	-		PP_3007	0.71	+0.1
3,401,050	-		PP_3007	0.71	+0.2
3,401,050	-		PP_3007	0.71	-0.7
3,401,188	-				-0.2
3,401,250	+				-2.4
3,401,251	-				-1.0
3,401,251	-				-0.9
3,401,251	-				-0.6
3,401,331	-				+0.7
3,401,379	-				+0.1
3,401,430	+				-0.8
3,401,431	-				+1.0
3,401,433	+				+1.1
3,401,433	+				-1.0
3,401,433	+				-0.5
3,401,434	-				+1.3
3,401,474	-		PP_3008	0.20	+0.3
3,401,491	+		PP_3008	0.26	-0.6
3,401,491	+		PP_3008	0.26	+0.6
3,401,492	-		PP_3008	0.26	-3.0
3,401,492	-		PP_3008	0.26	-1.2
3,401,492	-		PP_3008	0.26	-3.1
3,401,586	-		PP_3008	0.59	-0.6
3,401,586	-		PP_3008	0.59	-0.7
3,401,586	-		PP_3008	0.59	-0.7
3,401,658	-		PP_3008	0.84	-2.4
3,401,658	-		PP_3008	0.84	-0.1
3,401,686	-				+1.6
3,401,686	-				-1.1
3,401,804	+				+0.4
3,401,831	+		PP_3009	0.18	-1.7
3,401,832	-		PP_3009	0.19	-1.7
3,401,832	-		PP_3009	0.19	+1.5
3,401,835	-		PP_3009	0.22	+0.3
3,401,835	-		PP_3009	0.22	-0.5
3,401,835	-		PP_3009	0.22	-2.0
3,401,835	-		PP_3009	0.22	+1.6
3,401,835	-		PP_3009	0.22	-0.2
3,401,865	+		PP_3009	0.53	-0.5
3,401,866	-		PP_3009	0.54	+0.0
3,401,866	-		PP_3009	0.54	+1.1
3,401,885	+		PP_3009	0.73	+0.5
3,401,885	+		PP_3009	0.73	-0.4
3,401,885	+		PP_3009	0.73	+0.7
3,401,886	-		PP_3009	0.74	-2.5
3,401,886	-		PP_3009	0.74	-1.7
3,401,926	-				-1.2
3,401,933	-				+1.8
3,401,981	+				+0.9
3,401,981	+				+1.2
3,401,981	+				-1.5
3,401,982	-				+0.8
3,401,982	-				+0.7
3,401,982	-				-0.6
3,401,982	-				+1.0
3,401,983	+				-0.6
3,401,983	+				-2.1
3,401,983	+				+0.9
3,401,983	+				-2.9
3,401,983	+				+1.7
3,401,984	-				-2.1
3,401,984	-				-1.2
3,401,985	+				-0.2
3,401,985	+				-1.4
3,401,985	+				+0.2
3,401,986	-				-2.3
3,401,986	-				-0.1
3,402,011	+				-1.4
3,402,012	-				-3.3
3,402,140	-				+0.4
3,402,213	+		PP_3010	0.28	-0.7
3,402,214	-		PP_3010	0.29	+0.6
3,402,215	+		PP_3010	0.29	-2.3
3,402,216	-		PP_3010	0.29	+0.7
3,402,216	-		PP_3010	0.29	+1.0
3,402,216	-		PP_3010	0.29	-1.8
3,402,216	-		PP_3010	0.29	-2.4
3,402,250	-		PP_3010	0.38	+1.7
3,402,274	+		PP_3010	0.45	+0.0
3,402,275	-		PP_3010	0.45	+0.0
3,402,295	-		PP_3010	0.51	-0.2
3,402,312	-		PP_3010	0.55	+0.1
3,402,367	+		PP_3010	0.70	-0.0
3,402,367	+		PP_3010	0.70	+1.3
3,402,367	+		PP_3010	0.70	-0.4
3,402,367	+		PP_3010	0.70	-0.2
3,402,368	-		PP_3010	0.70	-0.4
3,402,408	+		PP_3010	0.81	+0.6
3,402,409	-		PP_3010	0.82	-0.5
3,402,409	-		PP_3010	0.82	+0.5
3,402,427	-		PP_3010	0.86	+1.1
3,402,474	+				-0.1
3,402,474	+				+0.2
3,402,497	+				-0.1
3,402,622	+				+1.1
3,402,632	-				-0.6
3,402,668	+		PP_3011	0.11	-0.3
3,402,668	+		PP_3011	0.11	-0.9
3,402,669	-		PP_3011	0.11	+1.2
3,402,669	-		PP_3011	0.11	+1.1
3,402,669	-		PP_3011	0.11	+0.4