Key	Value
Created on	2015-06-25 11:27:04
Version	5
Minimum conting length	1,000
Number of contigs	19,954
Number of splits	22,155
Total nucleotides	37.87 Mb

Key

Value

Created on

2015-06-25 11:27:04

Version

Minimum conting length

1,000

Number of contigs

19,954

Number of splits

22,155

Total nucleotides

37.87 Mb

Key	Value
Created on	2015-06-25 11:27:04
Version	3
Split length	2,000
Number of contigs	19,954
Number of splits	22,155
Total nucleotides	37.87 Mb
K-mer size	4

Key

Value

Created on

2015-06-25 11:27:04

Version

Split length

2,000

Number of contigs

19,954

Number of splits

22,155

Total nucleotides

37.87 Mb

K-mer size

Bin	Num Contigs	N50	GC Content	Red.
DWH_O_desum	588	1,804	50.98%	5.70%
DWH_Cryptic	140	2,656	43.99%	0.00%
DWH_Unknown	442	5,010	41.53%	0.00%

Bin

Taxonomy

Total Size

Num Contigs

N50

GC Content

Compl.

Red.

DWH_O_desum

588

1,804

50.98%

5.70%

DWH_Cryptic

140

2,656

43.99%

0.00%

DWH_Unknown

442

5,010

41.53%

0.00%

Taxon call	Relative occurrence
None	97.01%
Pseudomonas fluorescens	0.37%
Herminiimonas arsenicoxydans	0.25%
Shewanella sediminis	0.25%
Moritella sp.	0.25%
Vibrio vulnificus	0.25%
Cellvibrio japonicus	0.12%
Rahnella aquatilis	0.12%
Saccharophagus degradans	0.12%
Shewanella oneidensis	0.12%
Vibrio cholerae	0.12%
Colwellia psychrerythraea	0.12%
Nitrosomonas europaea	0.12%
Ferrimonas balearica	0.12%
Shewanella violacea	0.12%
Shewanella halifaxensis	0.12%
Brevibacillus brevis	0.12%
Prochlorothrix hollandica	0.12%
gamma proteobacterium	0.12%

File	Location
Contigs FASTA	bin_by_bin/DWH_Unknown/DWH_Unknown-contigs.fa
abundance	bin_by_bin/DWH_Unknown/DWH_Unknown-abundance.txt
functions	bin_by_bin/DWH_Unknown/DWH_Unknown-functions.txt
num_contigs	bin_by_bin/DWH_Unknown/DWH_Unknown-num_contigs.txt
Dupont_et_al	bin_by_bin/DWH_Unknown/DWH_Unknown-Dupont_et_al-hmm-sequences.txt
original_split_names	bin_by_bin/DWH_Unknown/DWH_Unknown-original_split_names.txt
variability	bin_by_bin/DWH_Unknown/DWH_Unknown-variability.txt
normalized_coverage	bin_by_bin/DWH_Unknown/DWH_Unknown-normalized_coverage.txt
relative_abundance	bin_by_bin/DWH_Unknown/DWH_Unknown-relative_abundance.txt
N50	bin_by_bin/DWH_Unknown/DWH_Unknown-N50.txt
Alneberg_et_al	bin_by_bin/DWH_Unknown/DWH_Unknown-Alneberg_et_al-hmm-sequences.txt
Campbell_et_al	bin_by_bin/DWH_Unknown/DWH_Unknown-Campbell_et_al-hmm-sequences.txt
portion_covered	bin_by_bin/DWH_Unknown/DWH_Unknown-portion_covered.txt
percent_redundancy	bin_by_bin/DWH_Unknown/DWH_Unknown-percent_redundancy.txt
max_normalized_ratio	bin_by_bin/DWH_Unknown/DWH_Unknown-max_normalized_ratio.txt
total_length	bin_by_bin/DWH_Unknown/DWH_Unknown-total_length.txt
Creevey_et_al	bin_by_bin/DWH_Unknown/DWH_Unknown-Creevey_et_al-hmm-sequences.txt
percent_complete	bin_by_bin/DWH_Unknown/DWH_Unknown-percent_complete.txt
std_coverage	bin_by_bin/DWH_Unknown/DWH_Unknown-std_coverage.txt
GC_content	bin_by_bin/DWH_Unknown/DWH_Unknown-GC_content.txt
mean_coverage	bin_by_bin/DWH_Unknown/DWH_Unknown-mean_coverage.txt

Source	Percent completeness	Percent redundancy
Dupont et al	0.00%	0.00%
Alneberg et al	0.00%	0.00%
Campbell et al	0.00%	0.00%
Creevey et al	0.00%	0.00%

Taxon call	Relative occurrence
None	97.07%
Thalassolituus oleivorans	0.49%
Saccharophagus degradans	0.33%
marine gamma	0.33%
Idiomarina xiamenensis	0.16%
Shewanella sediminis	0.16%
gamma proteobacterium	0.16%
Idiomarina loihiensis	0.16%
Sporichthya polymorpha	0.16%
Glaciecola psychrophila	0.16%
Methylovorus sp.	0.16%
Leptospira licerasiae	0.16%
Vibrio fischeri	0.16%
Pseudomonas fluorescens	0.16%
Acaryochloris marina	0.16%

File	Location
Contigs FASTA	bin_by_bin/DWH_O_desum/DWH_O_desum-contigs.fa
abundance	bin_by_bin/DWH_O_desum/DWH_O_desum-abundance.txt
functions	bin_by_bin/DWH_O_desum/DWH_O_desum-functions.txt
num_contigs	bin_by_bin/DWH_O_desum/DWH_O_desum-num_contigs.txt
Dupont_et_al	bin_by_bin/DWH_O_desum/DWH_O_desum-Dupont_et_al-hmm-sequences.txt
original_split_names	bin_by_bin/DWH_O_desum/DWH_O_desum-original_split_names.txt
variability	bin_by_bin/DWH_O_desum/DWH_O_desum-variability.txt
normalized_coverage	bin_by_bin/DWH_O_desum/DWH_O_desum-normalized_coverage.txt
relative_abundance	bin_by_bin/DWH_O_desum/DWH_O_desum-relative_abundance.txt
N50	bin_by_bin/DWH_O_desum/DWH_O_desum-N50.txt
Alneberg_et_al	bin_by_bin/DWH_O_desum/DWH_O_desum-Alneberg_et_al-hmm-sequences.txt
Campbell_et_al	bin_by_bin/DWH_O_desum/DWH_O_desum-Campbell_et_al-hmm-sequences.txt
portion_covered	bin_by_bin/DWH_O_desum/DWH_O_desum-portion_covered.txt
percent_redundancy	bin_by_bin/DWH_O_desum/DWH_O_desum-percent_redundancy.txt
max_normalized_ratio	bin_by_bin/DWH_O_desum/DWH_O_desum-max_normalized_ratio.txt
total_length	bin_by_bin/DWH_O_desum/DWH_O_desum-total_length.txt
Creevey_et_al	bin_by_bin/DWH_O_desum/DWH_O_desum-Creevey_et_al-hmm-sequences.txt
percent_complete	bin_by_bin/DWH_O_desum/DWH_O_desum-percent_complete.txt
std_coverage	bin_by_bin/DWH_O_desum/DWH_O_desum-std_coverage.txt
GC_content	bin_by_bin/DWH_O_desum/DWH_O_desum-GC_content.txt
mean_coverage	bin_by_bin/DWH_O_desum/DWH_O_desum-mean_coverage.txt

Source	Percent completeness	Percent redundancy
Dupont et al	52.25%	1.80%
Alneberg et al	70.59%	8.82%
Campbell et al	58.27%	2.16%
Creevey et al	70.00%	10.00%

Taxon call	Relative occurrence
None	97.87%
Bordetella avium	0.53%
Escherichia coli	0.53%
Herminiimonas arsenicoxydans	0.53%
Idiomarina baltica	0.53%

File	Location
Contigs FASTA	bin_by_bin/DWH_Cryptic/DWH_Cryptic-contigs.fa
abundance	bin_by_bin/DWH_Cryptic/DWH_Cryptic-abundance.txt
functions	bin_by_bin/DWH_Cryptic/DWH_Cryptic-functions.txt
num_contigs	bin_by_bin/DWH_Cryptic/DWH_Cryptic-num_contigs.txt
Dupont_et_al	bin_by_bin/DWH_Cryptic/DWH_Cryptic-Dupont_et_al-hmm-sequences.txt
original_split_names	bin_by_bin/DWH_Cryptic/DWH_Cryptic-original_split_names.txt
variability	bin_by_bin/DWH_Cryptic/DWH_Cryptic-variability.txt
normalized_coverage	bin_by_bin/DWH_Cryptic/DWH_Cryptic-normalized_coverage.txt
relative_abundance	bin_by_bin/DWH_Cryptic/DWH_Cryptic-relative_abundance.txt
N50	bin_by_bin/DWH_Cryptic/DWH_Cryptic-N50.txt
Alneberg_et_al	bin_by_bin/DWH_Cryptic/DWH_Cryptic-Alneberg_et_al-hmm-sequences.txt
Campbell_et_al	bin_by_bin/DWH_Cryptic/DWH_Cryptic-Campbell_et_al-hmm-sequences.txt
portion_covered	bin_by_bin/DWH_Cryptic/DWH_Cryptic-portion_covered.txt
percent_redundancy	bin_by_bin/DWH_Cryptic/DWH_Cryptic-percent_redundancy.txt
max_normalized_ratio	bin_by_bin/DWH_Cryptic/DWH_Cryptic-max_normalized_ratio.txt
total_length	bin_by_bin/DWH_Cryptic/DWH_Cryptic-total_length.txt
Creevey_et_al	bin_by_bin/DWH_Cryptic/DWH_Cryptic-Creevey_et_al-hmm-sequences.txt
percent_complete	bin_by_bin/DWH_Cryptic/DWH_Cryptic-percent_complete.txt
std_coverage	bin_by_bin/DWH_Cryptic/DWH_Cryptic-std_coverage.txt
GC_content	bin_by_bin/DWH_Cryptic/DWH_Cryptic-GC_content.txt
mean_coverage	bin_by_bin/DWH_Cryptic/DWH_Cryptic-mean_coverage.txt

Source	Percent completeness	Percent redundancy
Dupont et al	0.00%	0.00%
Alneberg et al	0.00%	0.00%
Campbell et al	0.72%	0.00%
Creevey et al	0.00%	0.00%

Across Samples (14)

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_DI ...	MT_PR ...	SAG_C ...	SAG_O ...	SAG_O ...	Y_A6_ ...	Y_A6_ ...	...
DWH_O_desum	27.48	27.28	1.27	42.68	38.60	8.71	2.62	45.81	0.37	0.16	...
DWH_Cryptic	9.41	7.57	0.40	0.49	1.03	0.00	0.00	0.00	0.04	0.01	...
DWH_Unknown	1.59	0.97	0.04	0.09	0.21	0.04	26.92	0.02	0.03	0.02	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_DI ...	MT_PR ...	SAG_C ...	Y_A6_ ...	Y_A6_ ...	...
DWH_O_desum	13.72 Kb	9.94 Kb	127.15	35.68	93.77	0.04	0.12	0.06	...
DWH_Cryptic	2.72 Kb	1.76 Kb	16.81	0.00	0.47	0.00	0.00	0.00	...
DWH_Unknown	286.43	154.04	0.54	0.07	0.09	0.07	0.00	0.00	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_PR ...	...
DWH_O_desum	0.49	0.47	0.02	0.01	...
DWH_Cryptic	0.56	0.41	0.02	0.00	...
DWH_Unknown	0.61	0.38	0.00	0.00	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_DI ...	MT_PR ...	SAG_C ...	SAG_O ...	SAG_O ...	...
DWH_O_desum	0.13	0.13	0.01	0.02	0.01	0.01	0.01	0.11	...
DWH_Cryptic	0.04	0.04	0.00	0.00	0.00	0.00	0.00	0.00	...
DWH_Unknown	0.01	0.00	0.00	0.00	0.00	0.00	0.13	0.00	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_DI ...	MT_PR ...	...
DWH_O_desum	1.00	1.00	0.96	0.20	0.71	...
DWH_Cryptic	1.00	0.99	0.68	0.10	0.30	...
DWH_Unknown	1.00	0.99	0.14	0.02	0.08	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_DI ...	MT_PR ...	SAG_C ...	SAG_O ...	SAG_O ...	Y_A6_ ...	Y_A6_ ...	...
DWH_O_desum	2.77 Kb	1.94 Kb	29.09	18.42	36.69	3.42	0.11	0.30	0.02	0.02	...
DWH_Cryptic	949.54	539.37	9.21	0.21	0.98	0.00	0.00	0.00	0.00	0.00	...
DWH_Unknown	160.24	69.25	0.98	0.04	0.20	0.01	1.15	0.00	0.00	0.00	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_PR ...	...
DWH_O_desum	0.92	0.89	0.04	0.03	...
DWH_Cryptic	0.98	0.74	0.04	0.00	...
DWH_Unknown	0.97	0.63	0.01	0.00	...

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

Bin	MG_DI ...	MG_PR ...	MG_UN ...	MT_DI ...	MT_PR ...	SAG_C ...	SAG_O ...	SAG_O ...	Y_A6_ ...	Y_A6_ ...	...
DWH_O_desum	935.61	647.48	23.05	10.39	24.15	5.85	0.25	0.67	0.07	0.04	...
DWH_Cryptic	375.46	243.98	11.80	0.47	1.43	0.00	0.00	0.00	0.02	0.01	...
DWH_Unknown	67.94	40.18	2.26	0.12	0.43	0.06	1.00	0.00	0.02	0.01	...

Percent Recruitment

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	DWH_Cryptic	DWH_O_desum	DWH_Unknown	__splits_not_binned__
MG_DISTAL	8.32%	79.45%	6.00%	6.23%
MG_PROXIMAL	6.60%	77.81%	3.62%	11.97%
MG_UNCONTAMINATED	0.34%	3.54%	0.16%	95.97%
MT_DISTAL	0.35%	99.15%	0.27%	0.23%
MT_PROXIMAL	0.80%	97.64%	0.70%	0.86%
SAG_COLWELLIA	0.00%	26.32%	0.14%	73.54%
SAG_OCEANOSPIRILLALES_HWTA	0.00%	6.94%	93.05%	0.01%
SAG_OCEANOSPIRILLALES_HWTC	0.00%	99.79%	0.05%	0.16%
Y_A6_1284M	0.03%	0.98%	0.12%	98.87%
Y_A6_2174M	0.01%	0.44%	0.06%	99.49%
Y_A6_700M	0.00%	0.08%	0.02%	99.90%
Y_BM57_1174M	0.00%	0.08%	0.03%	99.89%
Y_BM57_1574M	0.01%	0.23%	0.05%	99.71%
Y_BM57_850M	0.00%	0.11%	0.05%	99.84%