The 4 gene cluster 'bins' that were sotred in the anvi'o pan database for 'Trichodesmium-pangenome' under the collection name "default", describe 7,776 gene clusters with 33,249 genes that were identified in 7 genomes.

Basics

Here are some of the details about the pan database, and genomes storage.
Pan DB for Trichodesmium-pangenome w/ 7 samples.
Key Value
Created on 2020-04-15 16:53:02
Version 15
Number of genes 33,249
Number of gene clusters 7,776
Partial genes excluded No
Minbit parameter 0.5
Gene cluster min occurrence parameter 1
MCL inflation parameter 2.0
NCBI blastp or DIAMOND? NCBI blastp
Number of genomes used 7
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 7
Functional annotation Available
Functional annotation sources Pfam
These are the list of genomes used in this pan database: TARA_AON_82_MAG_00128, TARA_AOS_82_MAG_00025, TARA_IOS_50_MAG_00050, TARA_MED_95_MAG_00101, TARA_PON_109_MAG_00034, Trichodesmium_erythraeum_IMS101, Trichodesmium_thiebautii_H9_4

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: Trichodesmium-pangenome_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, ANI_alignment_coverage, ANI_alignment_lengths, ANI_hadamard, ANI_percentage_identity, ANI_similarity_errors, ANI_full_percentage_identity.

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, Hydrogenase, Nitrogen_fixation, NarK_U, Nitrite reductase, Protein_hesA,_heterocyst, [NiFe]_hydrogenase_metallocenter_assembly_protein_HypC, [NiFe]_hydrogenase_metallocenter_assembly_protein_HypD, [NiFe]_hydrogenase_metallocenter_assembly_protein_HypE, [NiFe]_hydrogenase_nickel_incorporation_protein_HypA, [NiFe]_hydrogenase_nickel_incorporation-associated_protein_HypB, Uptake_[NiFe]_hydrogenase,_large_subunit_HyaB, Uptake_[NiFe]_hydrogenase,_small_subunit_HyaA, nifT, nifU, nifX, nifZ, nifD, nifK, nifH, nifEN, nifB, nifW, nifO, Nitrate_transporter, Catalyzes_nitrate_uptake, NirB_nitrate_assimilatory_pathway, Circadian_oscillating_polypeptide_COP23_precursor, Circadian_period_extender_Pex.

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, ANI_alignment_coverage, ANI_alignment_lengths, ANI_hadamard, ANI_percentage_identity, ANI_similarity_errors, ANI_full_percentage_identity.