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 |
Key | Value |
---|---|
Created on | Storage DB knows nothing :( |
Version | 7 |
Number of genomes described | 7 |
Functional annotation | Available |
Functional annotation sources | Pfam |
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
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.