The 1 gene cluster 'bins' that were sotred in the anvi'o pan database for 'Afipia broomeae homd HMT 559' under the collection name "DEFAULT", describe 6,382 gene clusters with 39,621 genes that were identified in 8 genomes.

Basics

Here are some of the details about the pan database, and genomes storage.
Pan DB for Afipia broomeae homd HMT 559 w/ 8 samples.
Key Value
Created on 2025-12-12 19:29:32
Version 16
Number of genes 39,621
Number of gene clusters 6,382
Partial genes excluded No
Minbit parameter 0.5
Gene cluster min occurrence parameter 1
MCL inflation parameter 10.0
NCBI blastp or DIAMOND? NCBI blastp
Additional parameters for sequence search
Number of genomes used 8
Items aditional data keys num_genomes_gene_cluster_has_hits, num_genes_in_gene_cluster, max_num_paralogs, SCG, functional_homogeneity_index, geometric_homogeneity_index, combined_homogeneity_index
Genomes storage
Key Value
Created on Storage DB knows nothing :(
Version 7
Number of genomes described 8
Functional annotation Available
Functional annotation sources COG20_FUNCTION, KEGG_Class, Pfam, CAZyme, COG20_CATEGORY, KOfam, COG20_PATHWAY, KEGG_Module, KEGG_BRITE
These are the list of genomes used in this pan database: Afipia_broomeae_str_ATCC_49717_id_GCA_000314675_2, Afipia_broomeae_str_AWTP1_7_id_GCA_003963205_1, Afipia_broomeae_str_MED728_id_GCA_002689225_1, Afipia_broomeae_str_MGYG_HGUT_03734_id_GCA_902488705_1, Afipia_broomeae_str_NBIMC_P1_C1_id_GCA_000568595_1, Afipia_broomeae_str_NBIMC_P1_C2_id_GCA_000568615_1, Afipia_broomeae_str_NBIMC_P1_C3_id_GCA_000568515_1, Afipia_broomeae_str_TMED4_id_GCA_002172955_1

Summary files for gene clusters

This was a full summary (i.e., the `--quick` flag has not been used), hence the gene clusters summary file is not succint by any means.

The summary file: Afipia_broomeae_homd_HMT_559_gene_clusters_summary.txt.gz

Misc Data

For layers

The directory misc data layers contains TAB-delimited files for additional data stored under the following data group names for each sample/layer found in the merged database: default.

The default data group, which often is added by anvi'o automatically and contains important information, contained these keys: total_length, gc_content, percent_completion, percent_redundancy, num_genes, avg_gene_length, num_genes_per_kb, singleton_gene_clusters, num_gene_clusters.

For items

The directory misc data items contains TAB-delimited files for additional data stored under the following data group names for each item found in the merged database: default.