Bins that were identified in the merged profile database 'WATER' and stored in the database as "MAGS" collection, describe 5 bins accountig for 7,190,052 nucleotides, which represent 16.85% of all nucleotides stored in the contigs database, and 16.85% of nucleotides stored in the profile database.
The merged profile database that was generated with the minimum contig length of 1,000 contained 23,758 contigs, which correspond to 100% of all contigs, and 100% of all nucleotides found in the contigs database.
Profile DB for WATER w/ 4 samples.
Key Value
Created on 2020-03-11 05:33:40
Version 34
Minimum contig length 1,000
Number of contigs 23,758
Number of splits 23,775
Total nucleotides 42.66 Mb
SNVs profiled 1
SCVs profiled 1
Contigs DB
Key Value
Created on 2020-03-11 05:33:40
Version 18
Split length 20,000
Number of contigs 23,758
Number of splits 23,775
Total nucleotides 42.66 Mb
K-mer size 4
Genes are called 1
Splits consider gene calls 1
Gene function sources KEGG_Class, EGGNOG_KEGG_MODULE, EGGNOG_EC_NUMBER, EGGNOG_KEGG_PATHWAYS, EGGNOG_GENE_FUNCTION_NAME, KOfam, COG_FUNCTION, EGGNOG_BiGG_REACTIONS, EGGNOG_KEGG_TC, Transfer_RNAs, EGGNOG_BEST_TAX, KeggGhostKoala, Pfam, EGGNOG_GO_TERMS, COG_CATEGORY, EGGNOG_KEGG_KO, KEGG_Module, VirSorter (db2), EGGNOG_CAZy, EGGNOG_BRITE, EGGNOG_BACT
Summary reformatted contig names False

No description is provided

Summary of of each bin. You can download the information below also as a TAB-delimited file. Here is another TAB-delimited file that reports data for each single profile (such as number of reads mapped, etc).

Bin Source Taxonomy Total Size Num Contigs N50 GC Content Compl. Red. SCG Domain
 
WATER_MAG_00001 anvi-refine 509 5,803 62.80% 2.82% bacteria
 
WATER_MAG_00002 anvi-merge-bins 504 2,589 29.78% 8.45% bacteria
 
WATER_MAG_00003 anvi-refine 891 1,871 62.24% 7.04% bacteria
 
WATER_MAG_00004 anvi-refine 1,062 1,692 59.90% 4.23% bacteria
 
WATER_MAG_00005 anvi-refine 438 1,661 31.25% 5.63% bacteria

TAB-delimited matrix file for std_coverage: bins_across_samples/std_coverage.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 6.26 5.22 3.13 7.88
 
WATER_MAG_00002 0.03 0.01 6.85 0.04
 
WATER_MAG_00003 2.27 2.10 2.29 3.24
 
WATER_MAG_00004 0.01 0.01 3.49 0.01
 
WATER_MAG_00005 2.92 5.43 4.83 2.57

TAB-delimited matrix file for mean_coverage: bins_across_samples/mean_coverage.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 12.92 9.78 4.65 17.42
 
WATER_MAG_00002 0.01 0.00 12.81 0.01
 
WATER_MAG_00003 2.65 2.28 2.99 4.66
 
WATER_MAG_00004 0.00 0.00 6.91 0.00
 
WATER_MAG_00005 3.42 7.90 7.69 2.70

TAB-delimited matrix file for mean_coverage_Q2Q3: bins_across_samples/mean_coverage_Q2Q3.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 12.61 9.41 4.28 17.20
 
WATER_MAG_00002 0.00 0.00 12.09 0.00
 
WATER_MAG_00003 2.24 1.87 2.64 4.25
 
WATER_MAG_00004 0.00 0.00 6.61 0.00
 
WATER_MAG_00005 2.88 7.17 7.18 2.15

TAB-delimited matrix file for max_normalized_ratio: bins_across_samples/max_normalized_ratio.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 0.93 0.63 0.39 0.98
 
WATER_MAG_00002 0.00 0.00 1.00 0.00
 
WATER_MAG_00003 0.52 0.40 0.83 0.80
 
WATER_MAG_00004 0.00 0.00 1.00 0.00
 
WATER_MAG_00005 0.32 0.73 0.98 0.19

TAB-delimited matrix file for relative_abundance: bins_across_samples/relative_abundance.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 0.32 0.21 0.13 0.34
 
WATER_MAG_00002 0.00 0.00 1.00 0.00
 
WATER_MAG_00003 0.20 0.15 0.33 0.31
 
WATER_MAG_00004 0.00 0.00 1.00 0.00
 
WATER_MAG_00005 0.14 0.32 0.45 0.08

TAB-delimited matrix file for detection: bins_across_samples/detection.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 0.98 0.97 0.91 0.98
 
WATER_MAG_00002 0.00 0.00 1.00 0.00
 
WATER_MAG_00003 0.74 0.70 0.83 0.90
 
WATER_MAG_00004 0.00 0.00 0.99 0.00
 
WATER_MAG_00005 0.78 0.93 0.94 0.70

TAB-delimited matrix file for abundance: bins_across_samples/abundance.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 3.57 2.55 1.54 3.87
 
WATER_MAG_00002 0.00 0.00 4.24 0.00
 
WATER_MAG_00003 0.73 0.59 0.99 1.04
 
WATER_MAG_00004 0.00 0.00 2.29 0.00
 
WATER_MAG_00005 0.95 2.06 2.54 0.60

TAB-delimited matrix file for variability: bins_across_samples/variability.txt

Bin WCCR_ ... WCCR_ ... WROL_ ... WROL_ ...
 
WATER_MAG_00001 19.23 12.55 1.93 28.84
 
WATER_MAG_00002 0.00 0.00 10.95 0.00
 
WATER_MAG_00003 1.54 0.76 0.52 3.69
 
WATER_MAG_00004 0.00 0.00 5.90 0.00
 
WATER_MAG_00005 3.14 17.14 12.57 1.73

This panel shows how much of the mapped data is recruited by each bin (and how much of the mapped data was not binned under 'splits_not_binned' column). The way these percents calculated is quite simple: summarize the mean coverage of each split in each bin, and normalize every bin with respect to each other. It is critical to remember that these values do not take the unasssambled data into account. This is how you should read this table: "X percent of all mapped reads in Sample Y mapped to splits that were binned into bin Z".

TAB-delimited matrix file for percent recruitment: bins_across_samples/bins_percent_recruitment.txt

Sample WATER_MAG_00001 WATER_MAG_00002 WATER_MAG_00003 WATER_MAG_00004 WATER_MAG_00005 __splits_not_binned__
WCCR_1913 11.75% 0.00% 5.04% 0.00% 2.96% 80.24%
WCCR_1916 6.22% 0.00% 2.88% 0.00% 4.59% 86.31%
WROL_1914 3.32% 8.59% 3.88% 11.14% 5.09% 67.98%
WROL_1915 9.44% 0.01% 4.98% 0.00% 1.37% 84.20%

An overview of genes and functions based on the information found in the contigs database. If you haven't assigned any functions, these tables will only contain coverages of ORFs across samples.

Bin Total Size Num Genes Identified Tabular data
 
WATER_MAG_00001 2,555 🔗 genes | gene_coverages | detection
 
WATER_MAG_00002 1,641 🔗 genes | gene_coverages | detection
 
WATER_MAG_00003 2,589 🔗 genes | gene_coverages | detection
 
WATER_MAG_00004 2,657 🔗 genes | gene_coverages | detection
 
WATER_MAG_00005 1,125 🔗 genes | gene_coverages | detection

This panel shows you the result of non-single copy gene hits in your bins and contigs for each HMM profile. Here is a table that shows the total number of HMM hits in each bin for each HMM search type (from bins_across_samples/hmm_hit_totals.txt):

Bin Ribosomal_RNAs Transfer_RNAs
 
WATER_MAG_00001 2 39
 
WATER_MAG_00002 2 35
 
WATER_MAG_00003 None 27
 
WATER_MAG_00004 None 22
 
WATER_MAG_00005 None 17

The distribution of each HMM item found in your HMM collections is shown below. Different search types will be presented in their cognate tabs.

HMM hits in bins for Ribosomal_RNAs (from bins_across_samples/hmms_Ribosomal_RNAs.txt):

Bin Archa ... Archa ... Archa ... Archa ... Bacte ... Bacte ... Bacte ... Eukar ... Eukar ... Eukar ... ...
 
WATER_MAG_00001 1 1 None None None None None None None None ...
 
WATER_MAG_00002 None 1 None None 1 None None None None None ...
 
WATER_MAG_00003 None None None None None None None None None None ...
 
WATER_MAG_00004 None None None None None None None None None None ...
 
WATER_MAG_00005 None None None None None None None None None None ...

HMM hits in bins for Transfer_RNAs (from bins_across_samples/hmms_Transfer_RNAs.txt):

Bin Ala_G ... Ala_G ... Ala_G ... Ala_G ... Arg_A ... Arg_A ... Arg_C ... Arg_C ... Arg_C ... Arg_C ... ...
 
WATER_MAG_00001 1 None 1 None 1 None None None 1 1 ...
 
WATER_MAG_00002 1 None None None 3 None 1 None None None ...
 
WATER_MAG_00003 None None 1 None 1 None None None 1 None ...
 
WATER_MAG_00004 None None None None None 1 None None None 1 ...
 
WATER_MAG_00005 None None None None 1 None 1 None None 1 ...

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, t_order, t_species, t_class, t_genus, t_phylum, t_domain, t_family.

The default data group, which often is added by anvi'o automatically and contains important information, contained these keys: total_reads_mapped, num_SNVs_reported.

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, t_order, t_species, t_class, t_genus, t_phylum, t_domain, t_family.