ERR13109766 · Gut microbiome

BACMIX_minion_v1_9_20230623_zymo_magbead_NZ1

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 (%)
Staphylococcus aureus	Staphylococcus	15.9142
Listeria monocytogenes	Listeria	12.6790
Escherichia coli	Escherichia	12.4990
Bacillus amyloliquefaciens	Bacillus	8.9747
Bacillus velezensis	Bacillus	7.7210
Salmonella enterica	Salmonella	7.1586
Limosilactobacillus fermentum	Limosilactobacillus	7.0860
Enterococcus faecium	Enterococcus	5.3476
Bacillus subtilis	Bacillus	4.5348
Enterococcus faecalis	Enterococcus	4.0974
Enterococcus hirae	Enterococcus	1.5961
Staphylococcus pseudintermedius	Staphylococcus	0.8273
Listeria ivanovii	Listeria	0.8171
Pseudomonas aeruginosa	Pseudomonas	0.7860
Bacillus cereus	Bacillus	0.7344
Shigella sonnei	Shigella	0.7014
Limosilactobacillus mucosae	Limosilactobacillus	0.6916
Limosilactobacillus oris	Limosilactobacillus	0.6270
Bacillus thuringiensis	Bacillus	0.6089
Shigella dysenteriae	Shigella	0.6025
Lactobacillus delbrueckii	Lactobacillus	0.5695
Listeria welshimeri	Listeria	0.5137
Listeria grayi	Listeria	0.4604
Escherichia fergusonii	Escherichia	0.3983
Limosilactobacillus gorillae	Limosilactobacillus	0.3947
Bacillus licheniformis	Bacillus	0.3896
Enterococcus avium	Enterococcus	0.3640
Lactobacillus psittaci	Lactobacillus	0.3630
Bacillus halotolerans	Bacillus	0.2786
Listeria innocua	Listeria	0.2419
Staphylococcus argensis	Staphylococcus	0.2268
Staphylococcus lugdunensis	Staphylococcus	0.2185
Limosilactobacillus reuteri	Limosilactobacillus	0.2137
Pseudomonas frederiksbergensis	Pseudomonas	0.1923
Enterococcus columbae	Enterococcus	0.1666
Staphylococcus haemolyticus	Staphylococcus	0.1521
Listeria seeligeri	Listeria	0.1458
Enterococcus alcedinis	Enterococcus	0.1402
Bacillus pumilus	Bacillus	0.1292
Listeria cornellensis	Listeria	0.1120
Enterococcus wangshanyuanii	Enterococcus	0.1112
Shigella flexneri	Shigella	0.1090
Staphylococcus sciuri	Staphylococcus	0.1041

Saved public metadata

{
  "run_accession": "ERR13109766",
  "study_accession": "PRJEB75753",
  "sample_accession": "SAMEA115615487",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "777355",
  "base_count": "1212897765",
  "fastq_bytes": "1145564442",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR131/066/ERR13109766/ERR13109766.fastq.gz",
  "sample_title": "BACMIX_minion_v1_9_20230623_zymo_magbead_NZ1",
  "scientific_name": "gut metagenome"
}

Public files

ERR13109766.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": "ca0460f57c5673bb1a4cc91e16e76e71b1e01ffacec33ef3e9a216621857a3e9",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1593.0,
  "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": 5914,
    "elapsed_seconds": 6.827886618000008,
    "reads_submitted": 30000,
    "reads_after_filter": 30000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 24,
      "fraction": 0.12,
      "adapters_found": {
        "27F": 24
      },
      "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."
}