ERR13464073 · Gut microbiome

GUTMCM_minion_v1_9_20240516_zymo_Z2_bc02

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 (%)
Faecalibacterium prausnitzii	Faecalibacterium	28.3606
Veillonella parvula	Veillonella	19.8602
Escherichia coli	Escherichia	17.2888
Veillonella rodentium	Veillonella	11.4595
Veillonella dispar	Veillonella	2.8490
Shigella dysenteriae	Shigella	2.3173
Clostridioides difficile	Clostridioides	2.0419
Fusobacterium nucleatum	Fusobacterium	2.0114
Roseburia intestinalis	Roseburia	1.9968
Roseburia hominis	Roseburia	1.5851
Veillonella seminalis	Veillonella	1.2613
Bacteroides fragilis	Bacteroides	1.0656
Bacteroides thetaiotaomicron	Bacteroides	0.8580
Prevotella intermedia	Prevotella	0.8517
Veillonella infantium	Veillonella	0.8418
Fusobacterium periodonticum	Fusobacterium	0.8011
Veillonella rogosae	Veillonella	0.7182
Shigella sonnei	Shigella	0.6616
Escherichia fergusonii	Escherichia	0.5141
Shigella flexneri	Shigella	0.4237
Prevotella corporis	Prevotella	0.4117
Prevotella nigrescens	Prevotella	0.2509
Fusobacterium simiae	Fusobacterium	0.2415
Veillonella atypica	Veillonella	0.2163
Veillonella tobetsuensis	Veillonella	0.2127
Bacteroides ovatus	Bacteroides	0.2035
Fusobacterium hwasookii	Fusobacterium	0.1875
Bacteroides timonensis	Bacteroides	0.1724
Limosilactobacillus fermentum	Limosilactobacillus	0.1489
Bacteroides cellulosilyticus	Bacteroides	0.0996
Veillonella caviae	Veillonella	0.0874

Saved public metadata

{
  "run_accession": "ERR13464073",
  "study_accession": "PRJEB59610",
  "sample_accession": "SAMEA115904656",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "473954",
  "base_count": "734769765",
  "fastq_bytes": "596409584",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/073/ERR13464073/ERR13464073.fastq.gz",
  "sample_title": "GUTMCM_minion_v1_9_20240516_zymo_Z2_bc02",
  "scientific_name": "gut metagenome"
}

Public files

ERR13464073.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": "9d3f4b8cd2e606fb96a01689b5a254e6c0d504e6855754f8d98fea333807e4bf",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1575.0,
  "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": 6435,
    "elapsed_seconds": 4.951471389999995,
    "reads_submitted": 30000,
    "reads_after_filter": 30000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 11,
      "fraction": 0.055,
      "adapters_found": {
        "27F": 11
      },
      "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."
}