seq update

andersen-lab · Dec 6, 2024 · b277065 · b277065
1 parent f3706fd
commit b277065
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Showing 4 changed files with 19 additions and 13 deletions.
diff --git a/Encina_sewage_seqs.csv b/Encina_sewage_seqs.csv
@@ -207,15 +207,15 @@ 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
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diff --git a/PointLoma_sewage_seqs.csv b/PointLoma_sewage_seqs.csv
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+2024-11-12,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.04,0.0,10.54,0.0,0.0,0.0,0.0,12.98,0.0,0.0,0.0,0.0,0.0,38.19,0.0,1.46,16.92,0.0,19.83
+2024-11-13,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,11.66,0.0,0.0,0.0,0.0,11.28,0.0,0.0,0.0,0.0,0.0,19.84,0.0,0.02,54.33,0.0,2.81
diff --git a/SouthBay_sewage_seqs.csv b/SouthBay_sewage_seqs.csv
@@ -191,8 +191,8 @@ 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
 2024-06-09,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,0.0,35.85,0.0,0.0,0.0,0.0,0.0,5.64,0.0,0.0,0.0,0.0,28.01,0.0,30.42,0.0,0.0,0.0
 2024-06-13,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.04,0.0,39.47,0.0,0.0,0.0,0.0,0.0,16.25,0.0,0.0,0.0,0.0,21.56,0.0,22.65,0.0,0.0,0.0
 2024-06-16,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.08,0.0,89.83,0.0,0.0,0.0,0.0,0.0,0.12,0.0,0.0,0.0,0.0,9.88,0.0,0.04,0.02,0.0,0.0
-2024-06-20,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,84.9,0.0,0.0,0.0,0.0,0.0,5.22,0.0,0.0,0.0,0.0,9.89,0.0,0.0,0.0,0.0,0.0
-2024-06-23,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.0,0.03,0.0,74.93,0.0,0.0,0.0,0.0,0.0,17.8,0.0,0.0,0.0,0.0,1.01,0.0,0.05,0.0,0.0,0.01
+2024-06-20,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,84.89,0.0,0.0,0.0,0.0,0.0,5.22,0.0,0.0,0.0,0.0,9.89,0.0,0.0,0.0,0.0,0.0
+2024-06-23,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.0,0.03,0.0,74.92,0.0,0.0,0.0,0.0,0.0,17.81,0.0,0.0,0.0,0.0,1.01,0.0,0.06,0.0,0.0,0.01
 2024-06-25,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,0.0,87.72,0.0,0.0,0.0,0.0,0.0,1.31,0.0,0.0,0.0,0.0,10.62,0.0,0.02,0.0,0.0,0.01
 2024-06-27,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,40.18,0.0,0.0,0.0,0.0,0.0,47.01,0.0,0.0,0.0,0.0,12.68,0.0,0.08,0.0,0.0,0.0
 2024-07-04,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.03,0.0,32.14,0.0,0.0,0.0,0.0,0.0,19.5,0.0,0.0,0.0,0.0,3.97,0.0,44.31,0.02,0.0,0.01
@@ -206,7 +206,7 @@ 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
 2024-08-01,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,30.46,0.0,0.0,0.0,0.0,0.0,47.44,0.0,0.0,0.0,0.0,11.63,0.0,0.96,7.98,0.0,1.38
 2024-08-04,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,0.0,33.5,0.0,0.0,0.0,0.0,0.0,60.95,0.0,0.0,0.0,0.0,0.59,0.0,1.27,3.54,0.0,0.01
 2024-08-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.08,0.0,38.67,0.0,0.0,0.0,0.0,0.0,36.08,0.0,0.0,0.0,0.0,5.28,0.0,16.0,3.86,0.0,0.0
-2024-08-11,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.06,0.0,53.61,0.0,0.0,0.0,0.0,0.0,20.18,0.0,0.0,0.0,0.0,13.29,0.0,7.19,1.21,0.0,0.01
+2024-08-11,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,0.0,0.0,0.0,0.06,0.0,54.69,0.0,0.0,0.0,0.0,0.0,19.1,0.0,0.0,0.0,0.0,13.29,0.0,7.19,1.21,0.0,0.01
 2024-08-13,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.04,0.0,23.59,0.0,0.0,0.0,0.0,0.0,35.67,0.0,0.0,0.0,0.0,5.66,0.0,2.34,19.8,0.0,0.01
 2024-08-15,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.09,0.0,34.4,0.0,0.0,0.0,0.0,0.0,52.27,0.0,0.0,0.0,0.0,2.49,0.0,0.17,10.5,0.0,0.0
 2024-08-20,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,7.71,0.0,0.0,0.0,0.0,0.0,17.07,0.0,0.0,0.0,0.0,0.01,0.0,52.81,18.02,0.0,0.0
@@ -217,7 +217,7 @@ 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
 2024-09-03,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.06,0.0,91.26,0.0,0.0,0.0,0.0,0.0,1.47,0.0,0.0,0.0,0.0,7.14,0.0,0.0,0.0,0.0,0.0
 2024-09-08,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.04,0.0,12.67,0.0,0.0,0.0,0.0,0.0,19.94,0.0,0.0,0.0,0.0,25.98,0.0,0.0,41.32,0.0,0.06
 2024-09-10,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,45.19,0.0,0.0,0.0,0.0,31.73,0.0,23.08,0.0,0.0,0.0
-2024-09-12,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.23,0.0,0.0,0.0,0.0,0.0,16.81,0.0,0.0,0.0,0.0,5.35,0.0,0.49,15.04,0.0,0.0
+2024-09-12,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.2,0.0,0.0,0.0,0.0,0.0,16.21,0.0,0.0,0.0,0.0,5.35,0.0,1.12,15.04,0.0,0.0
 2024-09-17,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,0.0,56.19,0.0,0.0,0.0,0.0,0.0,4.44,0.0,0.0,0.0,0.0,4.24,0.0,0.02,35.07,0.0,0.0
 2024-09-22,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.52,0.0,0.0,0.0,0.0,0.0,95.06,0.0,0.0,0.0,0.0,0.03,0.0,3.72,0.62,0.0,0.0
 2024-09-24,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,5.53,0.0,0.0,0.0,0.0,0.0,94.39,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
@@ -226,3 +226,4 @@ 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
 2024-10-22,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,4.77,0.0,0.0,15.67,0.0,79.55
 2024-10-29,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05,0.0,0.45,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,80.03,0.0,0.0,18.44,0.0,0.0
 2024-10-31,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.39,0.0,0.73,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.31,0.0,0.0,55.15,0.0,0.0
+2024-11-17,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,58.85,0.0,0.0,0.0,0.0,0.0,0.03,0.0,0.0,0.0,0.0,0.02,0.0,0.0,5.86,0.0,35.2
diff --git a/rel_growth_rates.csv b/rel_growth_rates.csv
@@ -1,6 +1,6 @@
 Lineage,Estimated Advantage,Bootstrap 95% interval
-XEC.X,10.6%,"[4.51% , 38.84%]"
-KP.3.1.1.X,4.3%,"[-3.12% , 14.41%]"
-KP.2.X,0.9%,"[-53.34% , 34.76%]"
-KP.3.X,-5.4%,"[-23.11% , 5.46%]"
-JN.1.X,-10.7%,"[-95.29% , 34.95%]"
+KP.2.X,9.6%,"[-13.58% , 36.82%]"
+XEC.X,7.5%,"[-1.67% , 25.22%]"
+KP.3.1.1.X,3.0%,"[-7.94% , 13.60%]"
+JN.1.X,0.2%,"[-33.82% , 32.65%]"
+KP.3.X,-8.7%,"[-48.06% , 35.57%]"