ERR13110289 · Gut microbiome

BACMIX_minion_v1_9_20230623_zymo_magbead_NZ2

complete

Gut analysis is paused. Unfinished samples are not negative results. This is a mixed-host collection, not a curated human-only cohort.

Open interactive sample report

Taxonomic abundances

Species	Genus	Abundance (%)
Escherichia coli	Escherichia	15.3896
Staphylococcus aureus	Staphylococcus	14.7999
Listeria monocytogenes	Listeria	11.3205
Salmonella enterica	Salmonella	8.9594
Bacillus amyloliquefaciens	Bacillus	8.2573
Bacillus velezensis	Bacillus	7.3119
Limosilactobacillus fermentum	Limosilactobacillus	6.5884
Enterococcus faecium	Enterococcus	5.2212
Enterococcus faecalis	Enterococcus	3.9499
Bacillus subtilis	Bacillus	3.8951
Enterococcus hirae	Enterococcus	1.3899
Listeria ivanovii	Listeria	0.9689
Pseudomonas aeruginosa	Pseudomonas	0.9113
Staphylococcus pseudintermedius	Staphylococcus	0.8645
Bacillus cereus	Bacillus	0.8542
Shigella sonnei	Shigella	0.8531
Lactobacillus delbrueckii	Lactobacillus	0.7123
Shigella dysenteriae	Shigella	0.7110
Limosilactobacillus mucosae	Limosilactobacillus	0.6049
Bacillus thuringiensis	Bacillus	0.5501
Escherichia fergusonii	Escherichia	0.5291
Limosilactobacillus oris	Limosilactobacillus	0.4962
Listeria welshimeri	Listeria	0.4578
Enterococcus avium	Enterococcus	0.4176
Limosilactobacillus gorillae	Limosilactobacillus	0.4071
Listeria grayi	Listeria	0.3920
Lactobacillus psittaci	Lactobacillus	0.3886
Bacillus licheniformis	Bacillus	0.3298
Listeria innocua	Listeria	0.3131
Staphylococcus lugdunensis	Staphylococcus	0.2564
Staphylococcus argensis	Staphylococcus	0.2149
Limosilactobacillus reuteri	Limosilactobacillus	0.2078
Bacillus halotolerans	Bacillus	0.2064
Pseudomonas frederiksbergensis	Pseudomonas	0.1979
Shigella flexneri	Shigella	0.1452
Enterococcus columbae	Enterococcus	0.1361
Staphylococcus haemolyticus	Staphylococcus	0.1279
Bacillus pumilus	Bacillus	0.1268
Enterococcus alcedinis	Enterococcus	0.1219
Listeria cornellensis	Listeria	0.1113
Staphylococcus sciuri	Staphylococcus	0.1085
Listeria seeligeri	Listeria	0.1069
Bacillus nakamurai	Bacillus	0.0872

Saved public metadata

{
  "run_accession": "ERR13110289",
  "study_accession": "PRJEB75753",
  "sample_accession": "SAMEA115615488",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "825323",
  "base_count": "1281131624",
  "fastq_bytes": "1210625821",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR131/089/ERR13110289/ERR13110289.fastq.gz",
  "sample_title": "BACMIX_minion_v1_9_20230623_zymo_magbead_NZ2",
  "scientific_name": "gut metagenome"
}

Public files

ERR13110289.fastq.gz

Analysis provenance

{
  "marker": "16S",
  "pipeline": "Archaions v18.8",
  "cohort": "Gut, mixed hosts; not curated as a human-only cohort",
  "execution_state": "paused_by_user",
  "sample_state": "complete",
  "read_sampling": "First available reads; not random subsampling",
  "input_sha256": "dfdc858b152ff526118ac14511db2684d7de984ad57f7a5958e557ad5830b6bd",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1591.0,
  "quality_scores": "No measured quality scores in fetched FASTA",
  "classifier_stats": {
    "marker": "16s",
    "pipeline": "v18.8",
    "gpu": "RTX-PRO-6000",
    "input_path": "volume-fastq-gz",
    "reads_in": 30000,
    "reads_skipped": 5696,
    "elapsed_seconds": 7.608285193,
    "reads_submitted": 30000,
    "reads_after_filter": 30000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 18,
      "fraction": 0.09,
      "adapters_found": {
        "27F": 18
      },
      "should_trim": true
    },
    "porechop_ran": false,
    "porechop_reason": "fast-path: no adapter trimming required"
  },
  "metadata_coverage": "Saved ENA run fields only. BioSample attributes, study abstracts and file MD5s have not been fetched for this panel."
}