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240801_SG_WW #202

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240801_SG_WW #202

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7c5863d
240801_SG_WW
Aug 5, 2024
79bd872
growth rate calc
CviewMachineAcct Aug 5, 2024
19fa446
2024-08-05_16-21-37_240805_ENC_PL_SB_WW_cumulative_since_2024-07-15_s…
CviewMachineAcct Aug 5, 2024
8fb2faa
2024-08-13_01-15-33_240812_ENC_PL_SB_WW_cumulative_since_2024-07-29_s…
CviewMachineAcct Aug 13, 2024
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6 changes: 6 additions & 0 deletions Encina_sewage_qPCR.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
7 changes: 7 additions & 0 deletions Encina_sewage_seqs.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
8 changes: 8 additions & 0 deletions PointLoma_sewage_qPCR.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
7 changes: 7 additions & 0 deletions PointLoma_sewage_seqs.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
6 changes: 6 additions & 0 deletions SouthBay_sewage_qPCR.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
3 changes: 3 additions & 0 deletions SouthBay_sewage_seqs.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
8 changes: 8 additions & 0 deletions rel_growth_rates.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
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