Tables documentation
Contents
Tables documentation¶
The data available here and consists of five different tables, which will be introduced on this page. This data collection consists of metadata for each of the sequencing datasets we retrieved, as well as the results of aligning reads to reference sequences from the ResFinder and Silva databases and accompanying diversity measurements.
Metadata¶
Files: metadata.sql, metadata.tsv, metadata.h5
Column |
Explanation |
Example |
|---|---|---|
run_accession |
Identifer for sequencing reads. |
DRR000836 |
sample_accession |
Identifer for sample. |
SAMD00002573 |
project_accession |
Identifer for project. |
PRJDA61421 |
country |
Locality of sample isolation: country names, oceans or seas, followed by regions and localities. |
N/A |
location |
Geographic location of isolation of the sample (latitude, longitude). |
N/A |
continent |
Geographic region (land or water body) |
N/A |
collection_date |
Date that the specimen was collected. |
2016-01-01 |
tax_id |
NCBI taxon ID of the organism from which the sample was obtained. |
939928 |
host |
Natural (as opposed to laboratory) host to the organism from which sample was obtained. |
Homo sapiens |
host_tax_id |
NCBI taxon ID of the host |
9606 |
instrument_platform |
Instrument platform used in sequencing experiment. |
LS454 |
instrument_model |
Instrument model used in sequencing experiment. |
454 GS FLX Titanium |
library_layout |
Sequencing library layout. |
SINGLE |
raw_reads |
Number of raw sequencing reads. |
1268608 |
trimmed_reads |
Number of trimmed sequencing reads. |
1247751 |
raw_bases |
Number of bases in the raw sequencing reads. |
641025182 |
trimmed_bases |
Number of bases in the trimmed sequencing reads. |
1247751 |
trimmed_fragments |
Number of trimmed read fragments that can be mapped. |
1247751 |
ARG counts¶
Files: ARG.sql, ARG.tsv, ARG.h5
Column |
Explanation |
Example |
|---|---|---|
run_accession |
Identifer for sequencing reads. |
DRR000836 |
sample_accession |
Identifer for sample. |
SAMD00002573 |
project_accession |
Identifer for project. |
PRJDA61421 |
trimmed_fragments |
Total number of fragments. |
1247751 |
run_date |
Date that KMA program ran. |
2020-11-10 |
kma_version |
Version of KMA used. |
1.3.0 |
refSequence |
Name of template sequence. |
blaACT-4_2_AJ311172 |
refSequence_length |
Length of template sequence in bp. |
1146 |
refCoveredPositions |
The number of covered positions in the template with a minimum depth of 1. |
427 |
refConsensusSum |
Total number of bases identical to the template. |
424 |
bpTotal |
Total number of bases aligned to the template. |
1651 |
fragmentCountAln |
Number of fragments mapped and aligned to the template. |
5 |
bacterial_fragment |
Sum of rRNA fragments mappped and aligned for the dataset. |
1428 |
ResFinder annotations¶
Files: ResFinder_anno.sql, ResFinder_anno.tsv, ResFinder_anno.h5 To group ARGs by classes, phenotypes or mechanisms, one can use the annotation table below. It contains the annotation given in the official documentation for the ResFinder database (link).
Column |
Explanation |
Example |
|---|---|---|
gene |
Name of gene (refSequence) |
aac(2’)-Ia_1_L06156 |
anno_type |
What type of label is given for the gene (Class, gene_length, Phenotype, Mechanism) |
Class |
anno_value |
The label for the annotation type |
Aminoglycoside |
rRNA counts¶
Files: rRNA.sql, rRNA.tsv, rRNA.h5
Column |
Explanation |
Example |
|---|---|---|
run_accession |
Identifer for sequencing reads. |
DRR000836 |
sample_accession |
Identifer for sample. |
SAMD00002573 |
project_accession |
Identifer for project. |
PRJDA61421 |
run_date |
Date that KMA program ran. |
2020-11-10 |
kma_version |
Version of KMA used. |
1.3.0 |
phylum_name |
Name of phylum. |
Bacteroidetes |
phylum_tax |
NCBI taxon ID of the phylum. |
976 |
genus_name |
Name of genus. |
Myroides |
genus_tax |
NCBI taxon ID of the genus. |
76831 |
fragmentCountAln |
Sum of fragments aligned to rRNA genes belonging to the corresponding genus. |
10.7744 |
Diversity measures¶
Files: diversity.sql, diversity.tsv, diversity.h5
Column |
Explanation |
Example |
|---|---|---|
run_accession |
Identifer for sequencing reads. |
DRR000836 |
kma_version |
Version of KMA used. |
1.3.0 |
category |
What group of genes the diversity measures are for: ARG, Phyla or Genera. |
ARG |
total_fragments |
Total fragments that could be mapped. |
1247751 |
category_fragments |
Number of fragments aligned to the category genes. |
6.6925 |
n |
Number of unique genes/taxon IDs in group (observed richness) |
3 |
Shannon |
Shannon diversity index for category |
0.887324 |
Simpson |
Simpson (1-D) diversity index for category |
0.604705 |