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Ignore outliers from Ginkgo Bioworks
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Ignores H1 and H3 records from Ginkgo Bioworks that have identical
collection and submission dates of July 24, 2024 and that most likely
represent a metadata error. We have emailed Ginkgo about the issue and
will revert this commit when the records in GISAID have been corrected.
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@huddlej
huddlej committed Aug 6, 2024
1 parent 67072f6 commit 8209b35
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132 changes: 132 additions & 0 deletions config/h1n1pdm/outliers.txt
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Expand Up @@ -20,6 +20,80 @@ A/Bolivia/346/2017
A/Bolivia/492/2017
A/Brest/1161/2014
A/California/07/2009NYMC-X18113/198
A/California/GKISBBBB21564/2024
A/California/GKISBBBB25876/2024
A/California/GKISBBBB36325/2024
A/California/GKISBBBB36910/2024
A/California/GKISBBBB38383/2024
A/California/GKISBBBB38474/2024
A/California/GKISBBBB39042/2024
A/California/GKISBBBB39946/2024
A/California/GKISBBBB39980/2024
A/California/GKISBBBB40002/2024
A/California/GKISBBBB40532/2024
A/California/GKISBBBB79478/2024
A/California/GKISBBBB79619/2024
A/California/GKISBBBB93637/2024
A/California/GKISBBBB94968/2024
A/California/GKISBBBB95744/2024
A/California/GKISBBBB96220/2024
A/California/GKISBBBC01461/2024
A/California/GKISBBBC05376/2024
A/California/GKISBBBC06960/2024
A/California/GKISBBBC07081/2024
A/California/GKISBBBC56054/2024
A/California/GKISBBBC56868/2024
A/California/H20-333-8347/2023
A/California/H20-333-9240/2023
A/California/H20-334-5449/2023
A/California/H20-335-3976/2023
A/California/H20-338-6209/2023
A/California/H20-338-6218/2023
A/California/H20-339-3179/2023
A/California/H20-339-4116/2023
A/California/H20-339-5511/2023
A/California/H20-339-8648/2023
A/California/H20-339-8694/2023
A/California/H20-339-8939/2023
A/California/H20-339-9265/2023
A/California/H20-343-7814/2023
A/California/H20-344-4698/2024
A/California/H20-344-8374/2023
A/California/H20-345-1930/2023
A/California/H20-346-1203/2023
A/California/H20-346-1296/2023
A/California/H20-346-1369/2023
A/California/H20-347-0182/2023
A/California/H20-347-0365/2023
A/California/H20-353-2074/2023
A/California/H20-354-3340/2024
A/California/H20-354-4518/2023
A/California/H20-355-6160/2024
A/California/H20-356-1715/2024
A/California/H20-356-3504/2024
A/California/H20-356-4655/2024
A/California/H20-356-4799/2024
A/California/H20-356-4843/2024
A/California/H20-356-8347/2024
A/California/H20-356-8492/2024
A/California/H20-357-2634/2024
A/California/H20-358-0384/2024
A/California/H20-358-0532/2024
A/California/H20-358-0781/2024
A/California/H20-358-5198/2024
A/California/H20-358-9034/2024
A/California/H20-360-0152/2024
A/California/H20-360-0869/2024
A/California/H20-360-3269/2024
A/California/H20-360-6337/2024
A/California/H20-361-1483/2024
A/California/H20-361-5421/2024
A/California/H20-361-5428/2024
A/California/H20-361-5880/2024
A/California/H20-361-7728/2024
A/California/H20-361-8337/2024
A/California/H20-362-0448/2024
A/California/H20-362-3957/2024
A/Cherkessk/2/2016
A/Christchurch/16/2010NIB-74xp13/202
A/Colorado/84/2022
Expand All @@ -29,6 +103,9 @@ A/Darwin/27/2021
A/Denmark/1/2021
A/Denmark/36/2021
A/EasternIndia/107/2009
A/Florida/GKISBBBB21197/2024
A/Florida/GKISBBBB31412/2024
A/Florida/GKISBBBC38471/2024
A/Galicia/2443/2017
A/Guatemala/150/2018
A/Hebei-haigang/SWL1572/2019
Expand Down Expand Up @@ -81,6 +158,17 @@ A/Montpellier/F_004_122_JL/2020
A/Netherlands/10407/2018
A/Netherlands/11985/2022
A/Netherlands/2425/2018
A/NewJersey/GKISBBBB61671/2024
A/NewJersey/GKISBBBC27445/2024
A/NewJersey/GKISBBBC56219/2024
A/NewYork/GKISBBBB51498/2024
A/NewYork/GKISBBBB61120/2024
A/NewYork/GKISBBBB61738/2024
A/NewYork/GKISBBBC17889/2024
A/NewYork/GKISBBBC25282/2024
A/NewYork/GKISBBBC25981/2024
A/NewYork/GKISBBBC29200/2024
A/NewYork/H20-339-2682/2023
A/NewYork/IVYG43Q01E4/2022
A/Ningxia-Xixia/SWL137/2020
A/Norway/1929/2014
Expand Down Expand Up @@ -140,7 +228,51 @@ A/Texas/14/2008
A/Tomsk/273-MA1/2010
A/Tyumen/1V/2018
A/Vietnam/102/2015
A/Virginia/GKISBBBB44934/2024
A/Virginia/GKISBBBB66753/2024
A/Virginia/GKISBBBC12377/2024
A/Virginia/GKISBBBC14156/2024
A/Virginia/GKISBBBC52690/2024
A/Virginia/H20-328-9855/2024
A/Virginia/H20-332-5086/2023
A/Virginia/H20-333-7609/2023
A/Virginia/H20-334-3495/2023
A/Virginia/H20-335-5111/2023
A/Virginia/H20-335-6689/2023
A/Virginia/H20-339-7786/2024
A/Virginia/H20-339-9942/2024
A/Virginia/H20-340-0104/2023
A/Virginia/H20-340-7006/2023
A/Virginia/H20-340-7050/2023
A/Virginia/H20-340-7362/2023
A/Virginia/H20-341-6809/2024
A/Virginia/H20-343-1450/2024
A/Virginia/H20-344-1904/2024
A/Virginia/H20-344-7605/2023
A/Virginia/H20-346-1416/2023
A/Virginia/H20-346-5169/2024
A/Virginia/H20-346-9496/2024
A/Virginia/H20-347-8165/2024
A/Virginia/H20-352-9351/2024
A/Virginia/H20-352-9930/2023
A/Virginia/H20-353-2956/2024
A/Virginia/H20-354-3303/2024
A/Virginia/H20-354-5080/2024
A/Virginia/H20-354-5413/2024
A/Virginia/H20-356-8674/2024
A/Virginia/H20-357-3763/2024
A/Virginia/H20-358-0448/2024
A/Virginia/H20-358-1322/2024
A/Virginia/H20-358-4611/2024
A/Virginia/H20-358-5692/2024
A/Washington/GKISBBBB54527/2024
A/Washington/GKISBBBB54556/2024
A/Washington/GKISBBBC06545/2024
A/Washington/GKISBBBC19329/2024
A/Washington/H20-344-6926/2023
A/Washington/H20-345-3037/2023
A/Wisconsin/28/2011
A/Wisconsin/87/2005
A/Yunnan-Hongta/SWL1618/2020
A/Yunnan-Longyang/SWL1982/2015
strain
86 changes: 86 additions & 0 deletions config/h3n2/outliers.txt
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Expand Up @@ -15,6 +15,48 @@ A/Brazil/BA-LACEN-BA071-292012660/2021
A/Brazil/BA-LACEN-BA123-292029844/2021
A/Brazil/BA-LACEN-BA128-292008241/2021
A/Busan/15453/2009
A/California/GKISBBBB23788/2024
A/California/GKISBBBB38009/2024
A/California/GKISBBBB50035/2024
A/California/GKISBBBB51219/2024
A/California/GKISBBBB61984/2024
A/California/GKISBBBB66295/2024
A/California/GKISBBBB67692/2024
A/California/GKISBBBB76533/2024
A/California/GKISBBBC05659/2024
A/California/H20-335-6480/2023
A/California/H20-335-7982/2023
A/California/H20-338-5849/2023
A/California/H20-338-5905/2023
A/California/H20-338-5913/2023
A/California/H20-338-5919/2023
A/California/H20-339-1788/2023
A/California/H20-339-3361/2023
A/California/H20-343-8387/2023
A/California/H20-345-0152/2023
A/California/H20-354-3298/2024
A/California/H20-355-3992/2024
A/California/H20-355-5771/2024
A/California/H20-355-5826/2024
A/California/H20-355-6255/2024
A/California/H20-356-3553/2023
A/California/H20-356-4987/2023
A/California/H20-356-7106/2024
A/California/H20-356-7819/2024
A/California/H20-356-8105/2024
A/California/H20-356-8108/2024
A/California/H20-356-8930/2024
A/California/H20-357-1481/2024
A/California/H20-357-1662/2024
A/California/H20-357-5690/2024
A/California/H20-358-5293/2024
A/California/H20-359-0246/2024
A/California/H20-360-4951/2024
A/California/H20-360-7042/2024
A/California/H20-360-7132/2024
A/California/H20-361-1238/2024
A/California/H20-361-6912/2024
A/California/H20-361-7668/2024
A/California/NHRC0001/2011
A/Cambodia/NHRCC00001/2009
A/Cambodia/NHRCC00002/2009
Expand Down Expand Up @@ -57,6 +99,10 @@ A/Delaware/3/2011
A/Delaware/33/2017
A/DistrictOfColumbia/2/2017
A/England/71140418/2017
A/Florida/GKISBBBB27685/2024
A/Florida/GKISBBBB31358/2024
A/Florida/GKISBBBB71431/2024
A/Florida/GKISBBBC62844/2024
A/Fujian-Fengze/1507/2017
A/Fujian-Licheng/1868/2016
A/Gangwon/11/1999
Expand Down Expand Up @@ -351,7 +397,18 @@ A/Nepal/21FL2237/2021
A/Nepal/S1825/2023
A/Netherlands/233/1982
A/NewJersey/53/2015
A/NewJersey/GKISBBBB78001/2024
A/NewJersey/GKISBBBC02510/2024
A/NewJersey/GKISBBBC26396/2024
A/NewJersey/GKISBBBC56943/2024
A/NewJersey/GKISBBBC92565/2024
A/NewMexico/19/2022
A/NewYork/GKISBBBB40239/2024
A/NewYork/GKISBBBB53238/2024
A/NewYork/GKISBBBB78363/2024
A/NewYork/GKISBBBC19243/2024
A/NewYork/GKISBBBC28046/2024
A/NewYork/H20-326-9986/2023
A/NorthDakota/19/2017
A/Novosibirsk/1/2019
A/OSAKA/31/2005
Expand Down Expand Up @@ -486,6 +543,34 @@ A/Taiwan/937/2009
A/Tasmania/308/2022
A/Tokyo/1/1975
A/Utah/10/2012
A/Virginia/GKISBBBB32085/2024
A/Virginia/GKISBBBB55311/2024
A/Virginia/GKISBBBB60785/2024
A/Virginia/GKISBBBB79305/2024
A/Virginia/GKISBBBC94570/2024
A/Virginia/H20-338-4322/2023
A/Virginia/H20-339-7732/2024
A/Virginia/H20-339-8173/2024
A/Virginia/H20-339-8387/2023
A/Virginia/H20-343-2085/2023
A/Virginia/H20-347-6421/2023
A/Virginia/H20-352-9162/2024
A/Virginia/H20-352-9636/2024
A/Virginia/H20-353-3953/2024
A/Virginia/H20-353-5543/2024
A/Virginia/H20-354-0008/2024
A/Virginia/H20-354-7016/2024
A/Virginia/H20-354-7058/2024
A/Virginia/H20-354-7061/2024
A/Virginia/H20-354-9986/2023
A/Virginia/H20-355-1126/2024
A/Virginia/H20-355-5372/2024
A/Virginia/H20-358-2226/2024
A/Virginia/H20-358-2704/2024
A/Virginia/H20-358-2945/2024
A/Washington/GKISBBBB53658/2024
A/Washington/GKISBBBB73119/2024
A/Washington/H20-356-0958/2024
A/WestVirginia/10/2012
A/WestVirginia/15/2012
A/WestVirginia/16/2012
Expand All @@ -512,3 +597,4 @@ A/Zhejiang-Wuxin/1916/2018
A/Zhejiang-Yongkang/1137/2018
A/Zhejiang-Yongkang/1567/2022
A/Zhejiang-Yongkang/1576/2022
strain

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