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Manually fix serotype mis-annotations (#62)
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Manually fix serotype annotations for genbank samples that were flagged
during nextclade (all) serotype testing.

#58 (comment)

Add comments to the annotations.tsv file to explain the changes.
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@j23414
j23414 authored Jun 4, 2024
1 parent f166d5d commit e5aa1c5
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Showing 2 changed files with 9 additions and 2 deletions.
7 changes: 7 additions & 0 deletions ingest/defaults/annotations.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -1001,3 +1001,10 @@ KR029565 serotype_genbank denv2 # Annotated as denv1 but matches denv2
FJ502850 serotype_genbank denv2 # Annotated as denv1 but matches denv2
AY612201 serotype_genbank denv2 # Annotated as denv1 but matches denv2
MT597439 serotype_genbank denv4 # Annotated as denv2 but is denv4 based on submitter article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7952331/ (isolate: 43257)
MN448607 serotype_genbank denv1 # Annotated as denv2 but blastn places within denv1
MZ284953 serotype_genbank denv1 # Annotated as organism="dengue virus type 3" but isolate="dev1"
MZ285732 serotype_genbank denv1 # Annotated as organism="dengue virus type 3" but isolate="dev1"
MZ285058 serotype_genbank denv2 # Annotated as organism="Dengue virus 4" but duplicate of NC_001474 (denv2)
MW332572 serotype_genbank denv2 # Annotated as organism="Dengue virus 4" but blastn places within denv2
MS631898 serotype_genbank denv4 # Annotated as organism="Dengue virus 2" but blastn places within denv4
MB466022 serotype_genbank denv4 # Annotated as organism="Dengue virus 2" but blastn places within denv4
4 changes: 2 additions & 2 deletions phylogenetic/config/exclude.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@ EF051521 # ZS01/01 # metadata issue
MT929160 # Vero # cell line
MH048676 # MS13002673 # too divergent
MH048674 # MS11011405 # too divergent
MN448607 # KDC0574A2_06/02/2011 # too divergent
ON046268 # 00178/03 # too divergent
ON046278 # 00759/12 # too divergent
ON046276 # 00988/11 # too divergent
Expand All @@ -41,7 +40,6 @@ ON046270 # 01224/04 # too divergent
ON046274 # 01231/10 # too divergent
ON046272 # 01488/09 # too divergent
ON046271 # 01542/04 # too divergent
MZ284953 # dev1 # too divergent
MZ215848 # DKE_121 # too divergent
MW946564 # SENDAK_HD_10674 # sylvatic
OK605757 # DENV2_1_DAK_HD_76395 # sylvatic
Expand Down Expand Up @@ -890,3 +888,5 @@ GU131859 # duplicate of GU131847
GU131867 # duplicate of GU131862
HQ332171 # duplicate of HQ332170
HQ332178 # duplicate of HQ332177
MS631898 # PAT
MB466022 # PAT

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