hedgehog outputs a csv file with taxon name and lineage set assigned, one line corresponding to each sequence in the fasta file provided.
The name of an input query sequence. Note that spaces and commas in sequence names (not a good idea to have these characters in sequence names in general) get replaced by underscores.
6-character long set name that is generated from the lineages that comprise a given set.
The full length extended hash for a given set, used for matching internal to hedgehog.
The lineage that is the most recent common ancestor of all lineages within a given set.
A human readable set description, combining the precision (mrca) and a unique identifier for a given set assignment.
How many lineages are present in a given lineage set.
The spike mutations that define the lineage set.
The number of conflicting equally likely assignments.
The proportion of potentially informative sites present/missing in a query sequence.
Version of hedgehog software run.
Version of pango designations included in the hedgehog model.
Either passed or failed min_length and max_ambiguity quality control.
Source of assignment, either from designation hash or via the custom pangoLEARN model.
taxon,set_name,set_hash,precision,set_description,lineage_count,spike_constellation,conflict,ambiguity_score,hedgehog_version,pango_version,status,note
test_B.1.371,2add08,2add08a569c4004e5d3b21906f8a716f,A,A_1,615,S:D614G,NA,NA,,1.0,v1.2.6,passed_qc,Assigned from designation hash.
test_B.1.617.2,3613c5,3613c54b4a4a42a10036fa7ec340baef,B.1.617.2,B.1.617.2,1,S:D614G|S:L452R|S:P681R|S:T19R|S:T478K,NA,NA,,1.0,v1.2.6,passed_qc,Assigned from designation hash.
test_B.4,bc4a34,bc4a34e19529392c6ad118601e0469c3,A,A_2,75,,0.0,1.0,1.0,v1.2.6,passed_qc,
test_B.1.1.7,2430b9,2430b919e9b5f418c6a13add9d3c1db8,B.1.1.7,B.1.1.7,1,S:A570D|S:D1118H|S:D614G|S:N501Y|S:P681H|S:S982A|S:T716I|del:21765:6|del:21991:3,0.0,1.0,1.0,v1.2.6,passed_qc,
Novel_B.1.617.2,3613c5,3613c54b4a4a42a10036fa7ec340baef,B.1.617.2,B.1.617.2,1,S:D614G|S:L452R|S:P681R|S:T19R|S:T478K,0.0,1.0,1.0,v1.2.6,passed_qc,
test_bad_seq,None,None,NA,NA,NA,NA,NA,NA,1.0,v1.2.6,fail,seq_len:12