The 1 gene cluster 'bins' that were sotred in the anvi'o pan database for 'Haemophilus parahaemolyticus homd HMT 945' under the collection name "DEFAULT", describe 3,125 gene clusters with 24,492 genes that were identified in 12 genomes.

Basics

Here are some of the details about the pan database, and genomes storage.
Pan DB for Haemophilus parahaemolyticus homd HMT 945 w/ 12 samples.
Key Value
Created on 2025-12-12 21:01:09
Version 16
Number of genes 24,492
Number of gene clusters 3,125
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 12
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 12
Functional annotation Available
Functional annotation sources KEGG_Module, COG20_CATEGORY, KEGG_Class, Pfam, COG20_PATHWAY, COG20_FUNCTION, CAZyme, KEGG_BRITE, KOfam
These are the list of genomes used in this pan database: Haemophilus_parahaemolyticus_str_C2006000788_id_GCA_003252925_1, Haemophilus_parahaemolyticus_str_C2010039593_id_GCA_003253075_1, Haemophilus_parahaemolyticus_str_CCUG_3716_id_GCA_002015035_1, Haemophilus_parahaemolyticus_str_ERR1474568_bin_54_CONCOCT_v1_1_MAG_id_GCA_938021905_1, Haemophilus_parahaemolyticus_str_ERR1600749_bin_17_id_GCA_905203035_1, Haemophilus_parahaemolyticus_str_FDAARGOS_1199_id_GCA_016889385_1, Haemophilus_parahaemolyticus_str_G321_id_GCA_000826045_1, Haemophilus_parahaemolyticus_str_HK385_id_GCA_000262265_1, Haemophilus_parahaemolyticus_str_NCTC10794_id_GCA_900450875_1, Haemophilus_parahaemolyticus_str_NCTC_8479_id_GCA_900450675_1, Haemophilus_parahaemolyticus_str_NEB129_id_GCA_008330025_1, Haemophilus_parahaemolyticus_str_OHS0002_id_GCA_030938875_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: Haemophilus_parahaemolyticus_homd_HMT_945_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.