Bins that were identified in single profile 'INFANT CLC MERGED' and stored in the database as "SUPERVISED" collection, describe 13 bins accountig for 34,658,621 nucleotides, which represent 96.90% of all nucleotides stored in the annotation database, and 96.90% of nucleotides stored in the profile database.
The single profile database that was generated with the minimum contig length of 1,000 contained 4,189 contigs, which correspond to 100% of all contigs, and 100% of all nucleotides found in the annotation database.
Profile DB for INFANT CLC MERGED w/ 11 samples.
Key Value
Created on 2015-05-30 12:31:57
Version 5
Minimum conting length 1,000
Number of contigs 4,189
Number of splits 4,861
Total nucleotides 35.77 Mb
Annotation DB
Key Value
Created on 2015-05-30 12:31:57
Version 3
Split length 20,000
Number of contigs 4,189
Number of splits 4,861
Total nucleotides 35.77 Mb
K-mer size 4

Summary of general characteristics of each bin.

Bin Taxonomy Total Size Num Contigs N50 GC Content Compl. Red.
 
E_faecalis 12 464,247 37.43% 6.00%
 
P_rhinitidis 20 237,220 30.27% 3.98%
 
P_avidum 28 279,435 63.41% 4.29%
 
S_epidermidis_pan 170 39,271 31.67% 9.70%
 
S_aureus 74 70,800 32.51% 7.76%
 
C_albicans 1,083 30,494 32.28% 64.90%
 
L_citreum 556 2,333 38.95% 4.18%
 
S_hominis 105 46,851 30.94% 6.60%
 
F_magna 526 2,137 32.84% 1.34%
 
Anaerococcus_sp 457 1,788 31.97% 3.67%
 
S_lugdunensis 252 15,609 33.37% 2.43%
 
S_pneumoniae 387 1,589 40.02% 2.35%
 
P_acnes 207 1,245 56.90% 0.00%

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 8.43 8.84 9.21 9.54 9.89 9.54 10.06 8.56 8.62 7.51 ...
 
P_rhinitidis 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.73 0.11 4.43 ...
 
P_avidum 0.59 0.11 0.05 0.00 0.00 0.00 0.00 0.25 0.42 0.42 ...
 
S_epidermidis_pan 2.32 1.90 1.73 1.60 1.12 1.37 0.84 0.70 1.30 0.38 ...
 
S_aureus 0.00 0.01 0.01 0.00 0.00 0.00 0.00 1.59 1.41 0.77 ...
 
C_albicans 0.01 0.06 0.03 0.08 0.09 0.06 0.05 0.00 0.00 0.00 ...
 
L_citreum 0.00 0.00 0.03 0.01 0.01 0.01 0.01 0.02 0.00 0.01 ...
 
S_hominis 0.12 0.25 0.18 0.02 0.12 0.27 0.18 0.08 0.06 0.08 ...
 
F_magna 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 ...
 
Anaerococcus_sp 0.06 0.01 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...
 
S_lugdunensis 0.00 0.10 0.11 0.00 0.00 0.00 0.01 0.00 0.01 0.02 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...
 
P_acnes 0.04 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 84.96 166.78 306.19 56.91 270.98 336.15 207.98 335.30 142.04 83.47 ...
 
P_rhinitidis 0.00 0.00 0.00 0.00 0.00 0.00 0.00 14.30 22.42 42.55 ...
 
P_avidum 1.03 0.34 0.07 0.00 0.00 0.00 0.00 0.46 19.33 0.04 ...
 
S_epidermidis_pan 525.41 673.93 674.56 48.25 275.82 569.45 215.91 287.79 152.79 99.04 ...
 
S_aureus 0.04 0.41 0.10 0.00 0.06 0.56 0.21 522.17 297.24 197.23 ...
 
C_albicans 0.00 6.78 0.04 2.03 67.54 5.18 7.52 0.00 0.02 0.00 ...
 
L_citreum 0.00 0.00 0.05 0.00 0.00 0.00 0.00 0.03 0.02 0.00 ...
 
S_hominis 6.08 16.50 16.33 0.30 11.32 11.74 8.20 7.39 9.01 1.55 ...
 
F_magna 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...
 
Anaerococcus_sp 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...
 
S_lugdunensis 0.27 0.74 1.28 0.02 0.56 0.45 0.22 0.28 0.45 0.02 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...
 
P_acnes 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 0.09 0.09 0.10 0.10 0.10 0.10 0.10 0.09 0.09 0.08 ...
 
P_rhinitidis 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.01 0.52 ...
 
P_avidum 0.16 0.03 0.01 0.00 0.00 0.00 0.00 0.07 0.12 0.11 ...
 
S_epidermidis_pan 0.16 0.13 0.12 0.11 0.08 0.10 0.06 0.05 0.09 0.03 ...
 
S_aureus 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.38 0.32 0.18 ...
 
C_albicans 0.01 0.16 0.07 0.08 0.30 0.22 0.15 0.00 0.00 0.00 ...
 
L_citreum 0.01 0.01 0.41 0.01 0.03 0.04 0.06 0.27 0.01 0.02 ...
 
S_hominis 0.07 0.19 0.14 0.00 0.09 0.21 0.14 0.06 0.03 0.04 ...
 
F_magna 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.12 0.00 0.00 ...
 
Anaerococcus_sp 0.84 0.05 0.09 0.00 0.00 0.00 0.00 0.01 0.00 0.00 ...
 
S_lugdunensis 0.00 0.41 0.53 0.00 0.00 0.00 0.01 0.00 0.00 0.04 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.02 ...
 
P_acnes 0.86 0.06 0.01 0.00 0.00 0.00 0.00 0.04 0.01 0.01 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 93.38 98.52 103.12 106.54 110.09 106.89 111.97 95.83 95.93 83.66 ...
 
P_rhinitidis 0.00 0.01 0.00 0.00 0.01 0.00 0.00 8.14 0.88 49.39 ...
 
P_avidum 6.52 1.19 0.50 0.00 0.00 0.00 0.00 2.83 4.64 4.64 ...
 
S_epidermidis_pan 23.99 19.79 18.15 15.80 11.63 14.35 8.69 7.32 13.30 3.90 ...
 
S_aureus 0.01 0.03 0.01 0.00 0.00 0.00 0.00 17.58 15.41 8.48 ...
 
C_albicans 0.03 0.55 0.21 0.31 0.95 0.62 0.50 0.00 0.00 0.00 ...
 
L_citreum 0.01 0.00 0.30 0.01 0.02 0.03 0.04 0.20 0.01 0.01 ...
 
S_hominis 1.03 2.70 1.93 0.03 1.31 2.94 1.98 0.81 0.39 0.60 ...
 
F_magna 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.00 0.00 ...
 
Anaerococcus_sp 0.33 0.02 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ...
 
S_lugdunensis 0.01 1.00 1.21 0.00 0.00 0.00 0.02 0.00 0.01 0.09 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.01 ...
 
P_acnes 0.24 0.02 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ...
 
P_rhinitidis 0.01 0.14 0.05 0.00 0.17 0.03 0.01 1.00 0.65 1.00 ...
 
P_avidum 0.99 0.96 0.88 0.01 0.01 0.01 0.01 0.99 0.98 0.99 ...
 
S_epidermidis_pan 0.90 0.90 0.90 0.81 0.90 0.90 0.90 0.90 0.87 0.87 ...
 
S_aureus 0.06 0.21 0.19 0.01 0.04 0.05 0.06 0.98 0.98 0.98 ...
 
C_albicans 0.18 0.71 0.67 0.26 0.87 0.87 0.77 0.04 0.03 0.01 ...
 
L_citreum 0.07 0.08 0.79 0.03 0.29 0.31 0.34 0.74 0.06 0.12 ...
 
S_hominis 0.77 0.93 0.96 0.08 0.92 0.95 0.93 0.92 0.50 0.67 ...
 
F_magna 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.54 0.01 0.02 ...
 
Anaerococcus_sp 0.47 0.18 0.31 0.00 0.00 0.01 0.01 0.06 0.01 0.00 ...
 
S_lugdunensis 0.08 0.85 0.93 0.00 0.01 0.04 0.21 0.02 0.09 0.34 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.08 ...
 
P_acnes 0.46 0.17 0.08 0.00 0.00 0.00 0.00 0.20 0.04 0.06 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 222.07 397.49 510.94 106.80 729.52 567.87 615.32 574.57 332.18 241.93 ...
 
P_rhinitidis 0.01 0.17 0.06 0.00 0.23 0.03 0.01 48.76 4.26 142.81 ...
 
P_avidum 15.56 4.97 2.73 0.02 0.01 0.01 0.01 16.98 16.21 13.47 ...
 
S_epidermidis_pan 61.00 85.65 95.91 17.88 82.70 81.56 51.37 47.06 50.30 12.37 ...
 
S_aureus 0.08 0.40 0.29 0.03 0.07 0.10 0.11 106.75 54.20 24.93 ...
 
C_albicans 0.29 2.76 1.43 0.92 6.79 3.60 3.24 0.05 0.08 0.02 ...
 
L_citreum 0.09 0.11 1.78 0.08 0.45 0.38 0.55 1.53 0.15 0.18 ...
 
S_hominis 3.10 11.44 9.95 0.27 9.14 16.07 11.28 5.15 2.45 2.44 ...
 
F_magna 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.90 0.04 0.04 ...
 
Anaerococcus_sp 1.53 0.34 0.50 0.00 0.00 0.01 0.02 0.08 0.02 0.00 ...
 
S_lugdunensis 0.12 4.56 6.35 0.01 0.02 0.05 0.36 0.03 0.27 0.73 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.15 0.14 ...
 
P_acnes 1.11 0.23 0.08 0.00 0.00 0.00 0.00 0.24 0.08 0.07 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 0.81 0.85 0.90 0.92 0.96 0.93 0.98 0.83 0.83 0.73 ...
 
P_rhinitidis 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.18 0.02 0.99 ...
 
P_avidum 0.32 0.06 0.02 0.00 0.00 0.00 0.00 0.14 0.23 0.23 ...
 
S_epidermidis_pan 0.88 0.72 0.67 0.61 0.48 0.59 0.35 0.30 0.53 0.15 ...
 
S_aureus 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.99 0.86 0.48 ...
 
C_albicans 0.03 0.52 0.22 0.28 0.95 0.68 0.49 0.00 0.00 0.00 ...
 
L_citreum 0.02 0.02 0.94 0.03 0.08 0.09 0.14 0.66 0.02 0.05 ...
 
S_hominis 0.32 0.83 0.61 0.01 0.40 0.91 0.61 0.25 0.11 0.18 ...
 
F_magna 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.00 ...
 
Anaerococcus_sp 1.00 0.07 0.13 0.00 0.00 0.00 0.00 0.01 0.00 0.00 ...
 
S_lugdunensis 0.00 0.78 0.97 0.00 0.00 0.00 0.01 0.00 0.01 0.08 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.02 ...
 
P_acnes 1.00 0.08 0.01 0.00 0.00 0.00 0.00 0.05 0.02 0.02 ...

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

Bin DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_1 ... DAY_2 ... DAY_2 ... DAY_2 ... ...
 
E_faecalis 52.37 113.29 83.98 35.85 151.90 89.26 119.91 85.60 87.03 51.09 ...
 
P_rhinitidis 0.07 0.45 0.24 0.04 0.53 0.15 0.06 12.18 4.33 66.78 ...
 
P_avidum 8.09 3.02 1.90 0.13 0.08 0.06 0.07 7.41 8.58 6.84 ...
 
S_epidermidis_pan 28.67 45.77 39.35 12.58 39.97 33.09 24.92 20.29 28.84 7.64 ...
 
S_aureus 0.34 0.94 0.71 0.27 0.33 0.40 0.40 25.01 21.81 10.03 ...
 
C_albicans 0.63 2.47 1.34 1.68 4.40 2.34 2.65 0.19 0.39 0.10 ...
 
L_citreum 0.25 0.30 1.33 0.29 0.75 0.57 0.82 1.23 0.47 0.44 ...
 
S_hominis 2.99 7.16 5.00 0.96 5.78 6.49 6.27 3.11 3.38 2.60 ...
 
F_magna 0.01 0.02 0.03 0.00 0.00 0.00 0.00 0.96 0.14 0.13 ...
 
Anaerococcus_sp 1.98 0.67 0.78 0.01 0.01 0.03 0.07 0.20 0.08 0.01 ...
 
S_lugdunensis 0.42 3.37 3.35 0.05 0.13 0.23 0.78 0.15 0.90 1.23 ...
 
S_pneumoniae 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.42 0.36 ...
 
P_acnes 1.39 0.45 0.22 0.00 0.00 0.01 0.01 0.45 0.26 0.20 ...

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 Anaerococcus_sp C_albicans E_faecalis F_magna L_citreum P_acnes P_avidum P_rhinitidis S_aureus S_epidermidis_pan S_hominis S_lugdunensis S_pneumoniae __splits_not_binned__
DAY_15A 1.29% 0.67% 58.80% 0.00% 0.09% 0.42% 3.89% 0.00% 0.02% 24.34% 0.83% 0.06% 0.00% 9.59%
DAY_15B 0.17% 3.83% 62.90% 0.00% 0.07% 0.05% 0.74% 0.02% 0.07% 20.42% 1.84% 1.31% 0.00% 8.58%
DAY_16 0.21% 1.63% 66.16% 0.00% 0.89% 0.02% 0.33% 0.01% 0.04% 18.71% 1.31% 1.49% 0.00% 9.21%
DAY_17A 0.01% 5.00% 65.68% 0.00% 0.19% 0.00% 0.01% 0.00% 0.02% 16.57% 0.17% 0.01% 0.00% 12.35%
DAY_17B 0.00% 6.03% 73.77% 0.00% 0.18% 0.00% 0.00% 0.02% 0.01% 12.60% 0.94% 0.00% 0.00% 6.45%
DAY_18 0.00% 3.94% 70.77% 0.00% 0.19% 0.00% 0.00% 0.00% 0.01% 15.32% 2.03% 0.01% 0.00% 7.72%
DAY_19 0.01% 3.58% 77.24% 0.00% 0.27% 0.00% 0.00% 0.00% 0.01% 9.72% 1.44% 0.08% 0.00% 7.65%
DAY_22A 0.03% 0.05% 64.90% 0.37% 0.67% 0.04% 1.81% 3.63% 12.64% 8.01% 0.59% 0.01% 0.00% 7.24%
DAY_22B 0.01% 0.14% 63.94% 0.03% 0.11% 0.02% 2.95% 0.54% 10.94% 14.59% 0.48% 0.09% 0.08% 6.08%
DAY_23 0.00% 0.04% 57.02% 0.04% 0.17% 0.02% 3.00% 22.20% 6.16% 4.39% 0.58% 0.31% 0.09% 5.97%
DAY_24 0.01% 0.19% 52.07% 1.72% 0.42% 0.01% 12.31% 14.80% 3.74% 7.94% 0.41% 0.10% 1.15% 5.12%

An overview of functions based on the information found in the annotation database.

Bin Total Size Num Genes Identified Functions Table
 
E_faecalis 2,589 🔗 Link
 
P_rhinitidis 1,136 🔗 Link
 
P_avidum 1,929 🔗 Link
 
S_epidermidis_pan 2,316 🔗 Link
 
S_aureus 2,420 🔗 Link
 
C_albicans 918 🔗 Link
 
L_citreum 1,325 🔗 Link
 
S_hominis 1,986 🔗 Link
 
F_magna 1,124 🔗 Link
 
Anaerococcus_sp 583 🔗 Link
 
S_lugdunensis 2,062 🔗 Link
 
S_pneumoniae 839 🔗 Link
 
P_acnes 378 🔗 Link

Hidden Markov Model Hits (none found)