taylorreiter
commented
1 year ago - qseqid: query sequence ID
- acceptor_group: the NCBI kingdom of the query (here, fungi)
- acceptor_max_bitscore: excluding self matches, the max bitscore for matches within the acceptor group
- acceptor_min_evalue: excluding self matches, the minimum e value for matches within the acceptor group
- acceptor_num_matches_per_group: excluding self matches, the number of matches to other proteins in the acceptor group
- acceptor_max_pident: excluding self matches, the maximum percent identity of matches within the acceptor group
- donor_group: potential donor group; the other NCBI kingdoms (plant, metazoa, other euks, virus, archaea, bacteria)
- donor_max_bitscore: the maximum bitscore among matches in each of the donor groups
- donor_min_evalue: the minimum evalue among matches in each of the donor groups
- donor_num_matches_per_group: the number of matches witihin each donor group
- donor_best_match: the protein accession for the best match within each donor group
- donor_best_match_lineage: the lineage of the best match within each donor group
- donor_best_match_pident: the percent identity for the best match within each donor group. Used to determine if contamination occurred (>80% pid == contamination likely)
- alien_index: a score of HGT probability based on e-value. > 0 possible HGT, >15 likely HGT, >45 highly likely HGT.
- hgt_index: a score of HGT probability based on bit score. Basically the same as alien index
- acceptor_lca_level: within the acceptor group, what level of taxonomy does the lowest common ancestor occur among all matches? If it’s at the phylum level, the HGT event is probably older than if it’s at the genus level. Or, if the HGT is only observed in two phyla, perhaps the HGT happened twice.
- donor_distribution_index: within the donor groups, how frequently does the HGT candidate occur in all the donor groups? Is it only seen in bacteria, or is it in bacterial, viruses, and archaea? >0.8 means more specific to a donor group.
- HGT_score: based on alien index and donor_best_match_pident, spells out the HGT prediction