diff --git a/Encina_sewage_qPCR.csv b/Encina_sewage_qPCR.csv index 8f51c53..5d31197 100644 --- a/Encina_sewage_qPCR.csv +++ b/Encina_sewage_qPCR.csv @@ -498,3 +498,9 @@ Sample_Date,Mean viral gene copies/L 07/24/24,3658463 07/25/24,5623675 07/26/24,8473028 +07/30/24,2904638 +07/31/24,3383188 +08/01/24,5961014 +08/02/24,4238903 +08/06/24,5162689 +08/09/24,6024119 diff --git a/Encina_sewage_seqs.csv b/Encina_sewage_seqs.csv index 8908906..317d8c7 100644 --- a/Encina_sewage_seqs.csv +++ b/Encina_sewage_seqs.csv @@ -206,7 +206,11 @@ Date,BA.1,BA.1.1.X,BA.2.X,BA.2.12.X,BA.4.X,BA.5.X,BA.2.75,BA.4.6,BQ.1.X,BQ.1.1.X 2024-06-10,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,76.14,0.0,0.0,0.0,0.0,17.84,0.0,0.0,0.0,0.0,0.0,6.01,0.0,0.0,0.0 2024-06-12,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,0.0,50.44,0.0,0.0,0.0,0.0,29.39,0.0,0.0,0.0,0.0,0.0,13.49,0.0,6.58,0.0 2024-06-19,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,30.72,0.0,0.0,0.0,0.0,51.42,0.0,0.0,0.0,0.0,0.0,0.39,0.0,7.89,0.0 +<<<<<<< HEAD +2024-06-20,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,78.24,0.0,0.0,0.0,0.0,5.04,0.0,0.0,0.0,0.0,0.0,0.54,0.0,0.01,11.15 +======= 2024-06-20,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,78.24,0.0,0.0,0.0,0.0,5.04,0.0,0.0,0.0,0.0,0.0,0.55,0.0,0.01,11.15 +>>>>>>> andersen_wastewater/master 2024-06-26,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,7.67,0.0,0.0,0.0,0.0,66.17,0.0,0.0,0.0,0.0,0.0,25.99,0.0,0.16,0.0 2024-06-28,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,4.96,0.0,0.0,0.0,0.0,70.35,0.0,0.0,0.0,0.0,0.0,11.07,0.0,0.57,13.0 2024-07-03,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,70.01,0.0,0.0,0.0,0.0,1.24,0.0,0.0,0.0,0.0,0.0,24.67,0.0,0.02,4.06 @@ -215,5 +219,8 @@ Date,BA.1,BA.1.1.X,BA.2.X,BA.2.12.X,BA.4.X,BA.5.X,BA.2.75,BA.4.6,BQ.1.X,BQ.1.1.X 2024-07-10,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.06,0.0,16.61,0.0,0.0,0.0,0.0,44.52,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.71,38.1 2024-07-17,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,5.79,0.0,0.0,0.0,0.0,18.22,0.0,0.0,0.0,0.0,0.0,4.59,0.0,16.69,54.66 2024-07-18,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,23.34,0.0,0.0,0.0,0.0,23.54,0.0,0.0,0.0,0.0,0.0,40.34,0.0,0.0,12.73 +<<<<<<< HEAD +======= 2024-07-25,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,31.12,0.0,0.0,0.0,0.0,32.62,0.0,0.0,0.0,0.0,0.0,23.6,0.0,0.29,12.37 2024-07-26,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,19.22,0.0,0.0,0.0,0.0,46.0,0.0,0.0,0.0,0.0,0.0,20.39,0.0,0.0,14.39 +>>>>>>> andersen_wastewater/master diff --git a/PointLoma_sewage_qPCR.csv b/PointLoma_sewage_qPCR.csv index 1ef25ab..18cd22c 100644 --- a/PointLoma_sewage_qPCR.csv +++ b/PointLoma_sewage_qPCR.csv @@ -589,3 +589,11 @@ Sample_Date,Mean viral gene copies/L 07/22/24,9038685 07/23/24,7320413 07/24/24,7188864 +07/28/24,9826146 +07/29/24,7132434 +07/30/24,7452637 +07/31/24,8171876 +08/04/24,9606389 +08/05/24,10952724 +08/06/24,13085052 +08/07/24,9558193 diff --git a/PointLoma_sewage_seqs.csv b/PointLoma_sewage_seqs.csv index 7d6703c..7e7fe90 100644 --- a/PointLoma_sewage_seqs.csv +++ b/PointLoma_sewage_seqs.csv @@ -434,7 +434,11 @@ Date,BA.1,BA.1.1.X,BA.2.X,BA.2.12.X,BA.4.X,BA.5.X,B.1.1.529,AY.113,AY.100,AY.20, 2024-05-20,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.11,0.0,81.42,0.0,0.0,0.0,0.0,8.03,0.0,0.0,0.0,0.0,0.0,0.0,0.0,10.44,0.0 2024-05-21,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,0.0,38.01,0.0,0.0,0.0,0.0,61.77,0.0,0.0,0.0,0.0,0.0,0.07,0.0,0.08,0.0 2024-05-22,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,97.53,0.0,0.0,0.0,0.0,0.25,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.22,0.0 +<<<<<<< HEAD +2024-05-26,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.1,0.0,91.28,0.0,0.0,0.0,0.0,7.51,0.0,0.0,0.0,0.0,0.0,1.01,0.0,0.05,0.0 +======= 2024-05-26,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.11,0.0,91.28,0.0,0.0,0.0,0.0,7.51,0.0,0.0,0.0,0.0,0.0,1.01,0.0,0.05,0.0 +>>>>>>> andersen_wastewater/master 2024-05-27,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.19,0.0,65.35,0.0,0.0,0.0,0.0,31.42,0.0,0.0,0.0,0.0,0.0,0.59,0.0,2.45,0.0 2024-05-28,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.0,0.0,45.96,0.0,0.0,0.0,0.0,0.11,0.0,0.0,0.0,0.0,0.0,0.36,0.0,53.52,0.0 2024-05-29,0.0,0.0,0.04,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.04,0.0,85.15,0.0,0.0,0.0,0.0,0.09,0.0,0.0,0.0,0.0,0.0,14.64,0.0,0.0,0.0 @@ -466,7 +470,10 @@ Date,BA.1,BA.1.1.X,BA.2.X,BA.2.12.X,BA.4.X,BA.5.X,B.1.1.529,AY.113,AY.100,AY.20, 2024-07-15,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,27.88,0.0,0.0,0.0,0.0,34.75,0.0,0.0,0.0,0.0,0.0,28.22,0.0,0.01,9.11 2024-07-16,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.03,0.0,36.77,0.0,0.0,0.0,0.0,41.79,0.0,0.0,0.0,0.0,0.0,8.24,0.0,0.08,13.02 2024-07-17,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,17.57,0.0,0.0,0.0,0.0,27.61,0.0,0.0,0.0,0.0,0.0,28.03,0.0,2.94,23.79 +<<<<<<< HEAD +======= 2024-07-21,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,15.47,0.0,0.0,0.0,0.0,69.68,0.0,0.0,0.0,0.0,0.0,11.12,0.0,0.0,3.73 2024-07-22,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.11,0.0,0.0,0.0,0.0,54.08,0.0,0.0,0.0,0.0,0.0,3.76,0.0,0.0,40.06 2024-07-23,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,17.73,0.0,0.0,0.0,0.0,33.63,0.0,0.0,0.0,0.0,0.0,7.89,0.0,0.0,40.75 2024-07-24,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,20.16,0.0,0.0,0.0,0.0,78.38,0.0,0.0,0.0,0.0,0.0,0.04,0.0,0.0,1.39 +>>>>>>> andersen_wastewater/master diff --git a/SouthBay_sewage_qPCR.csv b/SouthBay_sewage_qPCR.csv index 0cf25f4..ee10b03 100644 --- a/SouthBay_sewage_qPCR.csv +++ b/SouthBay_sewage_qPCR.csv @@ -309,3 +309,9 @@ Sample_Date,Mean viral gene copies/L 07/23/24,1363317 07/25/24,1211985 07/28/24,1172250 +07/30/24,829715 +08/01/24,1675094 +08/04/24,1416240 +08/06/24,1661929 +08/08/24,2438691 +08/11/24,2494514 diff --git a/SouthBay_sewage_seqs.csv b/SouthBay_sewage_seqs.csv index 2062728..0d82022 100644 --- a/SouthBay_sewage_seqs.csv +++ b/SouthBay_sewage_seqs.csv @@ -201,5 +201,8 @@ Date,BA.1,BA.1.1.X,BA.2.X,BA.2.12.X,BA.4.X,BA.5.X,BA.2.75,BA.4.6,BQ.1.X,BQ.1.1.X 2024-07-14,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,39.35,0.0,0.0,0.0,0.0,0.0,53.09,0.0,0.0,0.0,0.0,2.48,0.0,5.06,0.0 2024-07-18,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.0,0.01,0.0,22.47,0.0,0.0,0.0,0.0,0.0,28.7,0.0,0.0,0.0,0.0,35.58,0.0,13.21,0.0 2024-07-21,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.03,0.0,9.99,0.0,0.0,0.0,0.0,0.0,72.93,0.0,0.0,0.0,0.0,6.3,0.0,1.68,9.05 +<<<<<<< HEAD +======= 2024-07-23,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,35.01,0.0,0.0,0.0,0.0,0.0,18.65,0.0,0.0,0.0,0.0,0.0,0.0,0.0,46.33 2024-07-25,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.02,0.0,14.85,0.0,0.0,0.0,0.0,0.0,20.75,0.0,0.0,0.0,0.0,21.02,0.0,13.59,29.76 +>>>>>>> andersen_wastewater/master diff --git a/rel_growth_rates.csv b/rel_growth_rates.csv index 01a146a..39ce8a9 100644 --- a/rel_growth_rates.csv +++ b/rel_growth_rates.csv @@ -1,6 +1,14 @@ Lineage,Estimated Advantage,Bootstrap 95% interval +<<<<<<< HEAD +KP.3.1.1.X,12.3%,"[0.45% , 32.57%]" +KP.3.X,4.5%,"[-1.32% , 9.97%]" +KP.2.X,1.6%,"[-3.97% , 6.98%]" +KP.1.1.X,-3.1%,"[-53.80% , 5.96%]" +JN.1.X,-6.3%,"[-11.63% , 0.34%]" +======= KP.3.1.1.X,15.1%,"[-2.56% , 38.49%]" KP.2.X,4.1%,"[-2.74% , 13.56%]" KP.3.X,-2.6%,"[-8.57% , 3.60%]" KP.1.1.X,-3.0%,"[-8.33% , 1.66%]" JN.1.X,-4.1%,"[-8.63% , 0.62%]" +>>>>>>> andersen_wastewater/master