The 1 gene cluster 'bins' that were sotred in the anvi'o pan database for 'Streptococcus sobrinus homd HMT 768' under the collection name "DEFAULT", describe 2,702 gene clusters with 51,890 genes that were identified in 25 genomes.

Basics

Here are some of the details about the pan database, and genomes storage.
Pan DB for Streptococcus sobrinus homd HMT 768 w/ 25 samples.
Key Value
Created on 2025-12-13 00:46:06
Version 16
Number of genes 51,890
Number of gene clusters 2,702
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 25
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 25
Functional annotation Available
Functional annotation sources Pfam, KEGG_BRITE, KEGG_Class, COG20_PATHWAY, KEGG_Module, KOfam, COG20_CATEGORY, CAZyme, COG20_FUNCTION
These are the list of genomes used in this pan database: Streptococcus_sobrinus_str_1001283B150210_160208_F1_id_GCA_015669055_1, Streptococcus_sobrinus_str_10919_id_GCA_003172975_1, Streptococcus_sobrinus_str_ATCC_33478_id_GCA_000439045_1, Streptococcus_sobrinus_str_DSM_20742_id_GCA_000347935_1, Streptococcus_sobrinus_str_DSM_20742_id_GCA_000686605_1, Streptococcus_sobrinus_str_ERR589515_bin_80_CONCOCT_v1_1_MAG_id_GCA_937927005_1, Streptococcus_sobrinus_str_KCOM_1157_id_GCA_002266475_1, Streptococcus_sobrinus_str_NCTC10921_id_GCA_900475365_1, Streptococcus_sobrinus_str_NCTC12279_id_GCA_900475395_1, Streptococcus_sobrinus_str_NIDR_6715_15_id_GCA_003176815_1, Streptococcus_sobrinus_str_NIDR_6715_7_id_GCA_003176795_1, Streptococcus_sobrinus_str_SL1_id_GCA_003172995_1, Streptococcus_sobrinus_str_SRR7721897_bin_27_id_GCA_905199975_1, Streptococcus_sobrinus_str_TCI_107_id_GCA_000228065_2, Streptococcus_sobrinus_str_TCI_118_id_GCA_000228545_2, Streptococcus_sobrinus_str_TCI_124_id_GCA_000228125_2, Streptococcus_sobrinus_str_TCI_13_id_GCA_000227805_2, Streptococcus_sobrinus_str_TCI_200_id_GCA_000228665_2, Streptococcus_sobrinus_str_TCI_355_id_GCA_000228245_2, Streptococcus_sobrinus_str_TCI_357_id_GCA_000228265_2, Streptococcus_sobrinus_str_TCI_366_id_GCA_000228305_2, Streptococcus_sobrinus_str_TCI_384_id_GCA_000228445_2, Streptococcus_sobrinus_str_TCI_77_id_GCA_000227965_2, Streptococcus_sobrinus_str_TCI_79_id_GCA_000227985_2, Streptococcus_sobrinus_str_W1703_id_GCA_000467915_2

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: Streptococcus_sobrinus_homd_HMT_768_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.