summary.tsv¶
Classifications provided by the GTDB-Tk are in the files <prefix>.bac120.summary.tsv and <prefix>.ar53.summary.tsv for bacterial and archaeal genomes, respectively. These are tab separated files with the following columns:
user_genome: Unique identifier of query genome taken from the FASTA file of the genome.
classification: GTDB taxonomy string inferred by the GTDB-Tk. An unassigned species (i.e.,
s__) indicates that the query genome is either i) placed outside a named genus or ii) the ANI to the closest intra-genus reference genome with an AF >=0.65 is not within the species-specific ANI circumscription radius.closest_genome_reference: indicates the accession number of the reference genome (species) to which a user genome was assigned based on ANI and AF. ANI values are only calculated when a query genome is placed within a defined genus and are evaluated for all reference genomes in that genus.
closest_genome_reference_radius: indicates the species-specific ANI circumscription radius of the reference genomes used to determine if a query genome should be classified to the same species as the reference.
closest_genome_taxonomy: indicates the GTDB taxonomy of the above reference genome.
closest_genome_ani: indicates the ANI between the query and above reference genome.
closest_genome_af: indicates the alignment fraction (AF) between the query and above reference genome.
closest_placement_reference: indicates the accession number of the reference genome when a genome is placed on a terminal branch.
closest_placement_taxonomy: indicates the GTDB taxonomy of the above reference genome.
closest_placement_ani: indicates the ANI between the query and above reference genome.
closest_placement_af: indicates the alignment fraction (AF) between the query and above reference genome.
pplacer_taxonomy: indicates the pplacer taxonomy of the query genome.
classification_method: indicates the rule used to classify the genome. This field will be one of: i) ANI, indicating a species assignement was based solely on the calculated ANI and AF with a reference genome; ii) ANI/Placement, indicating a species assignment was made based on both ANI and the placement of the genome in the reference tree; iii) taxonomic classification fully defined by topology, indicating that the classification could be determine based solely on the genome’s position in the reference tree; or iv) taxonomic novelty determined using RED, indicating that the relative evolutionary divergence (RED) and placement of the genome in the reference tree were used to determine the classification.
note: provides additional information regarding the classification of the genome. Currently this field is only filled out when a species determination is made and indicates if the placement of the genome in the reference tree and closest reference according to ANI/AF are the same (congruent) or different (incongruent).
other_related_references: lists up to the 100 closest reference genomes based on ANI. ANI calculations are only performed between a query genome and reference genomes in the same genus.
msa_percent: indicates the percentage of the MSA spanned by the genome (i.e. percentage of columns with an amino acid).
red_value: indicates, when required, the relative evolutionary divergence (RED) for a query genome. RED is not calculated when a query genome can be classified based on ANI.
warnings: indicates unusual characteristics of the query genome that may impact the taxonomic assignment.
Produced by¶
Example¶
user_genome classification fastani_reference fastani_reference_radius fastani_taxonomy fastani_ani fastani_af closest_placement_reference closest_placement_taxonomy closest_placement_ani closest_placement_af pplacer_taxonomy classification_method note other_related_references(genome_id,species_name,radius,ANI,AF) aa_percent translation_table red_value warnings
genome_2 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365 GCA_002498365.1 95.0 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365 99.16 0.94 GCA_002498365.1 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365 99.16 0.94 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__ ANI/Placement topological placement and ANI have congruent species assignments GCA_002505345.1, s__VadinCA11 sp002505345, 95.0, 89.92, 0.89; GCA_002509405.1, s__VadinCA11 sp002509405, 95.0, 88.13, 0.89 87.1 11 N/A N/A
genome_3 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365 GCA_002498365.1 95.0 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365 95.33 0.87 GCA_002498365.1 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365 95.33 0.87 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__ ANI/Placement topological placement and ANI have congruent species assignments GCA_002505345.1, s__VadinCA11 sp002505345, 95.0, 94.26, 0.87; GCA_002509405.1, s__VadinCA11 sp002509405, 95.0, 90.74, 0.77 73.07 11 N/A N/A
genome_1 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium GCF_000024185.1 95.0 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium 100.0 1.0 GCF_000024185.1 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium 100.0 1.0 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__ ANI/Placement topological placement and ANI have congruent species assignments GCA_900321995.1, s__Methanobrevibacter sp900321995, 95.0, 80.9, 0.7; GCF_900114585.1, s__Methanobrevibacter olleyae, 95.0, 79.96, 0.55; GCA_900314635.1, s__Methanobrevibacter sp900314635, 95.0, 78.45, 0.3 97.09 11 N/A N/A