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Update h5n1-cattle-outbreak dropped strains
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The SRA accession matching isn't perfect since some NCBI GenBank records
just don't have linked accessions. Adding duplicate strains from the
Andersen lab data based on the sample ids in the strain names.
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joverlee521 committed Jun 6, 2024
1 parent 5690492 commit e4a25ba
Showing 1 changed file with 11 additions and 1 deletion.
12 changes: 11 additions & 1 deletion config/dropped_strains_h5n1-cattle-outbreak.txt
Original file line number Diff line number Diff line change
@@ -1,3 +1,14 @@
# Duplicated entries from Andersen Lab
A/Cattle/USA/24-008749-004-v/2024 # Duplicate of A/cattle/Texas/24-008749-004/2024
A/Cattle/USA/24-008749-006-original/2024 # Duplicate of A/cattle/Texas/24-008749-006-original/2024
A/Cattle/USA/24-008749-006-v/2024 # Duplicate of A/cattle/Texas/24-008749-006-original/2024
A/Cattle/USA/24-008766-001-original/2024 # Duplicate of A/cattle/Kansas/24-008766-001/2024
A/Cattle/USA/24-008766-001-v/2024 # Duplicate of A/cattle/Kansas/24-008766-001/2024
A/Cattle/USA/24-009027-002-original/2024 # Duplicate of A/cattle/Michigan/24-009027-002/2024
A/Cattle/USA/24-009027-002-v/2024 # Duplicate of A/cattle/Michigan/24-009027-002/2024
A/PEFA/USA/24-005915-001-original/2024 # Duplicate of A/Peregrinefalcon/California/24-005915-001/2024
A/Skunk/USA/24-006483-001-original/2024 # Duplicate of A/skunk/NewMexico/24-006483-001/2024

# Dropping these strains from include due to excess private mutations
A/cattle/NorthCarolina/24-010327-002/2024
A/cattle/Texas/24-009495-007/2024
Expand Down Expand Up @@ -86,4 +97,3 @@ A/turkey/SouthDakota/24-007379-002/2024
A/turkeyvulture/California/24-007419-001/2024
A/westerngull/California/24-004708-001/2024
A/woodduck/NorthCarolina/W24-026/2024

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