Annotation and quantitation of shotgun metagenomic sequence data
Generated by: George Edward Chlipala
Report date: April 2, 2021
Overview
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Output Files
| File | Description | Type |
|---|---|---|
| taxa_raw_counts.zip | ZIP archive of taxonomic summaries from phylum to species level result - raw sequence counts | result |
| taxa_raw_counts.xlsx | Excel spreadsheet of taxonomic summaries from phylum to species level result - raw sequence counts | result |
| taxa_normalized.zip | ZIP archive of taxonomic summaries from phylum to species level result - normalized as CPM | result |
| taxa_normalized.xlsx | Excel spreadsheet of taxonomic summaries from phylum to species level result - normalized as CPM | result |
| taxa_normalized_archaea.xlsx | Excel spreadsheet of taxonomic summaries from phylum to species level for archaea - normalized as CPM | result |
| taxa_normalized_archaea.zip | ZIP archive of taxonomic summaries from phylum to species level for archaea - normalized as CPM | result |
| taxa_normalized_bacteria.xlsx | Excel spreadsheet of taxonomic summaries from phylum to species level for bacteria - normalized as CPM | result |
| taxa_normalized_bacteria.zip | ZIP archive of taxonomic summaries from phylum to species level for bacteria - normalized as CPM | result |
| taxa_normalized_fungi.xlsx | Excel spreadsheet of taxonomic summaries from phylum to species level for fungi - normalized as CPM | result |
| taxa_normalized_fungi.zip | ZIP archive of taxonomic summaries from phylum to species level for fungi - normalized as CPM | result |
| taxa_normalized_virus.xlsx | Excel spreadsheet of taxonomic summaries from phylum to species level for virus - normalized as CPM | result |
| taxa_normalized_virus.zip | ZIP archive of taxonomic summaries from phylum to species level for virus - normalized as CPM | result |
| funl_raw_counts.xlsx | Excel spreadsheet of funtional gene summaries - raw sequence counts | result |
| funl_table.txt | Counts table of functional genes (orthologs) in TSV format | result |
| funl_table.biom | Counts table of functional genes (orthologs) in BIOM format. | result |
| funl_raw_counts.zip | ZIP archive of functional gene summaries - raw sequence counts | result |
| funl_filtered_raw_counts.xlsx | Excel spreadsheet of filtered funtional gene summaries - raw sequence counts | result |
| funl_filtered_table.txt | Filtered counts table of functional genes (orthologs) in TSV format | result |
| funl_table_filtered.biom | Filtered counts table of functional genes (orthologs) in BIOM format. | result |
| funl_filtered_raw_counts.zip | ZIP archive of filtered functional gene summaries - raw sequence counts | result |
Details
- Method: Centrifuge
-
References were matched using Centrifuge via a nucleotide search. - Reference sequence database (nucleotide) : nt
-
NCBI Genbank non-redundant nucleotide database
Figure 1. Summary of phyla per sample
Table 1. Summary of taxonomic alignments Download table data
| Stats | Raw reads | Total taxonomic alignments | Percent | Phylum sum (all alignments) | Percent |
|---|---|---|---|---|---|
| A.1 | 250000 | 91132 | 0.364528 | 90219 | 0.360876 |
| A.2 | 250000 | 92523 | 0.370092 | 91584 | 0.366336 |
| B.1 | 250000 | 95923 | 0.383692 | 94979 | 0.379916 |
| B.2 | 250000 | 93265 | 0.37306 | 92384 | 0.369536 |
Table 2. Summary of phyla Download table data
| Taxon | Counts | Percent |
|---|---|---|
| sk_Bacteria;k__Bacteria incertae sedis;p__Proteobacteria | 166428 | 45.08% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Actinobacteria | 97260 | 26.35% |
| sk_Eukaryota;k__Metazoa;p__Chordata | 16337 | 4.43% |
| Unassigned;Other;Other | 13917 | 3.77% |
| sk_Bacteria;Other;Other | 9244 | 2.50% |
| sk_Eukaryota;k__Viridiplantae;p__Streptophyta | 7975 | 2.16% |
| sk_Eukaryota;k__Fungi;p__Ascomycota | 5805 | 1.57% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Firmicutes | 4876 | 1.32% |
| sk_Eukaryota;k__Metazoa;p__Arthropoda | 4291 | 1.16% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Eukaryota incertae sedis | 4209 | 1.14% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Acidobacteria | 3869 | 1.05% |
| sk_Eukaryota;k__Metazoa;p__Nematoda | 3278 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Planctomycetes | 3186 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Euryarchaeota | 2986 | < 1% |
| sk_Eukaryota;k__Viridiplantae;p__Chlorophyta | 2610 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Bacteroidetes | 2567 | < 1% |
| sk_Eukaryota;Other;Other | 2177 | < 1% |
| sk_Eukaryota;k__Fungi;p__Basidiomycota | 2176 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Deinococcus-Thermus | 1922 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Platyhelminthes | 1680 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Cyanobacteria | 1665 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Verrucomicrobia | 1418 | < 1% |
| sk_Viruses;k__Viruses incertae sedis;p__Viruses incertae sedis | 1208 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Chloroflexi | 1093 | < 1% |
| sk_Eukaryota;k__Metazoa;Other | 1081 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Gemmatimonadetes | 1067 | < 1% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Apicomplexa | 957 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Nitrospirae | 443 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Thaumarchaeota | 428 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Chlorobi | 313 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Spirochaetes | 299 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Armatimonadetes | 177 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Mollusca | 170 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Crenarchaeota | 151 | < 1% |
| s__uncultured prokaryote;Other;Other | 132 | < 1% |
| sk_Eukaryota;k__Viridiplantae;Other | 126 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Synergistetes | 112 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Cnidaria | 108 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Bacteria incertae sedis | 102 | < 1% |
| sk_Eukaryota;k__Fungi;Other | 89 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Priapulida | 88 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Kiritimatiellaeota | 79 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Thermotogae | 69 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Chlamydiae | 68 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Echinodermata | 66 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Tenericutes | 60 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__candidate division NC10 | 58 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Aquificae | 48 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Acetothermia | 47 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Fusobacteria | 43 | < 1% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Bacillariophyta | 42 | < 1% |
| s__synthetic construct;Other;Other | 41 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Porifera | 35 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Annelida | 33 | < 1% |
| sk_Eukaryota;k__Fungi;p__Mucoromycota | 33 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Chrysiogenetes | 29 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Calditrichaeota | 25 | < 1% |
| s__unidentified;Other;Other | 23 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Ignavibacteriae | 20 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Fibrobacteres | 20 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Deferribacteres | 19 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Peregrinibacteria | 17 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Hemichordata | 15 | < 1% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Eustigmatophyceae | 14 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Thermodesulfobacteria | 14 | < 1% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Euglenida | 14 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Brachiopoda | 13 | < 1% |
| sk_Eukaryota;k__Fungi;p__Chytridiomycota | 13 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Saccharibacteria | 13 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Elusimicrobia | 13 | < 1% |
| sk_Eukaryota;k__Fungi;p__Microsporidia | 10 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Beckwithbacteria | 9 | < 1% |
| sk_Archaea;Other;Other | 9 | < 1% |
| s__uncultured prokaryote AT5;Other;Other | 8 | < 1% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Phaeophyceae | 7 | < 1% |
| sk_Viruses;Other;Other | 7 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Coprothermobacterota | 7 | < 1% |
| s__uncultured marine microorganism HF4000_ANIW137J11;Other;Other | 6 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__candidate division WWE3 | 6 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Dictyoglomi | 6 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Cloacimonetes | 5 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Placozoa | 4 | < 1% |
| s__uncultured marine microorganism HF4000_APKG8L7;Other;Other | 4 | < 1% |
| s__uncultured organism CA878;Other;Other | 4 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Rotifera | 4 | < 1% |
| s__uncultured marine microorganism HF4000_APKG5H11;Other;Other | 3 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Candidatus Korarchaeota | 3 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Caldiserica | 3 | < 1% |
| s__uncultured marine microorganism HF4000_005I08;Other;Other | 3 | < 1% |
| sk_Eukaryota;k__Fungi;p__Fungi incertae sedis | 3 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Wolfebacteria | 2 | < 1% |
| s__uncultured marine microorganism HF4000_009L19;Other;Other | 2 | < 1% |
| sk_Eukaryota;k__Fungi;p__Blastocladiomycota | 2 | < 1% |
| s__uncultured organism CA37;Other;Other | 2 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Tardigrada | 2 | < 1% |
| s__uncultured organism CA915;Other;Other | 2 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Nanoarchaeota | 2 | < 1% |
| s__uncultured marine microorganism HF4000_ANIW93N21;Other;Other | 2 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Nemertea | 2 | < 1% |
| s__uncultured prokaryote 2E01B;Other;Other | 2 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Ctenophora | 2 | < 1% |
| s__Shuttle vector pXsp8;Other;Other | 1 | < 1% |
| s__uncultured marine microorganism HF4000_APKG2H5;Other;Other | 1 | < 1% |
| sk_Eukaryota;k__Metazoa;p__Chaetognatha | 1 | < 1% |
| sk_Eukaryota;k__Fungi;p__Zoopagomycota | 1 | < 1% |
| s__uncultured marine microorganism HF4000_APKG8C21;Other;Other | 1 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Candidatus Micrarchaeota | 1 | < 1% |
| s__Cloning vector pABCc-mob;Other;Other | 1 | < 1% |
| s__uncultured marine microorganism HF4000_ANIW137I15;Other;Other | 1 | < 1% |
| s__Plasmid pFKY4;Other;Other | 1 | < 1% |
| sk_Eukaryota;k__Eukaryota incertae sedis;p__Xanthophyceae | 1 | < 1% |
| s__uncultured marine microorganism HF4000_ANIW137G21;Other;Other | 1 | < 1% |
| s__Cloning vector pAB34;Other;Other | 1 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Melainabacteria | 1 | < 1% |
| s__uncultured organism pXylP;Other;Other | 1 | < 1% |
| s__uncultured marine microorganism HF4000_APKG10H12;Other;Other | 1 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Campbellbacteria | 1 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Woesebacteria | 1 | < 1% |
| s__uncultured marine microorganism HF4000_137B17;Other;Other | 1 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Curtissbacteria | 1 | < 1% |
| s__Shuttle vector pDA71;Other;Other | 1 | < 1% |
| s__uncultured organism pCelD;Other;Other | 1 | < 1% |
| s__Broad host range vector vector pCVD019;Other;Other | 1 | < 1% |
| sk_Archaea;k__Archaea incertae sedis;p__Archaea incertae sedis | 1 | < 1% |
| s__Vector pATMTNF1;Other;Other | 1 | < 1% |
| s__uncultured marine microorganism HF4000_APKG1C9;Other;Other | 1 | < 1% |
| sk_Bacteria;k__Bacteria incertae sedis;p__Candidatus Berkelbacteria | 1 | < 1% |
| s__uncultured marine microorganism HF4000_APKG10F17;Other;Other | 1 | < 1% |
| s__uncultured organism pCelK;Other;Other | 1 | < 1% |
| s__uncultured marine microorganism HF4000_APKG2J17;Other;Other | 1 | < 1% |
Details
- Method: DIAMOND
-
References were matched using DIAMOND via a translated nucleotide search. - Method: Taxonomic filter
-
Custom ParametersData are filtered to retain reads associated with particular taxa. - regex = \sUnassigned,sk_Archaea,sk_Bacteria,k__Fungi,sk_Viruses
- Reference sequence database (protein) : swissprot
-
UniProt Swiss-Prot manually annotated and reviewed protein database.
Figure 1. Summary of high level functional annotations per sample
Table 1. Summary of functional annotation Download table data
| Stats | Raw reads (functional) | Total functional alignments | Percent | Subsystem level 1 sum | Percent | Filtered subsystem level 1 sum | Percent |
|---|---|---|---|---|---|---|---|
| A.1 | 500000 | 38692 | 0.077384 | 83415 | 0.16683 | 51681 | 0.103362 |
| A.2 | 500000 | 38400 | 0.0768 | 82516 | 0.165032 | 51372 | 0.102744 |
| B.1 | 500000 | 36549 | 0.073098 | 75633 | 0.151266 | 48689 | 0.097378 |
| B.2 | 500000 | 36411 | 0.072822 | 75756 | 0.151512 | 47806 | 0.095612 |
Table 2. Summary of high level functional annotations Download table data
| Level 1 category | Counts | Percent |
|---|---|---|
| 09100 Metabolism | 130178 | 41.02% |
| 09180 Brite Hierarchies | 95904 | 30.22% |
| 09120 Genetic Information Processing | 25125 | 7.92% |
| 09160 Human Diseases | 18578 | 5.85% |
| 09130 Environmental Information Processing | 16423 | 5.18% |
| 09150 Organismal Systems | 10861 | 3.42% |
| 09140 Cellular Processes | 10739 | 3.38% |
| 09190 Not Included in Pathway or Brite | 9476 | 2.99% |
| Unassigned | 36 | < 1% |