SRR28257770 · Gut microbiome

SRR28257770

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	29.0787
Enterobacter hormaechei	Enterobacter	24.7572
Enterobacter asburiae	Enterobacter	6.9554
Roseateles depolymerans	Roseateles	5.7187
Klebsiella pneumoniae	Klebsiella	4.8615
Klebsiella michiganensis	Klebsiella	3.9955
Enterobacter roggenkampii	Enterobacter	2.8199
Shigella dysenteriae	Shigella	2.6337
Roseateles chitosanitabidus	Roseateles	2.5475
Enterobacter mori	Enterobacter	2.1800
Enterobacter bugandensis	Enterobacter	2.0631
Enterobacter cloacae	Enterobacter	2.0457
Shigella sonnei	Shigella	1.9301
Romboutsia lituseburensis	Romboutsia	1.4537
Enterobacter ludwigii	Enterobacter	1.2829
Klebsiella aerogenes	Klebsiella	0.7928
Escherichia fergusonii	Escherichia	0.7327
Roseateles saccharophilus	Roseateles	0.6435
Enterobacter kobei	Enterobacter	0.4679
Citrobacter freundii	Citrobacter	0.4393
Roseateles oligotrophus	Roseateles	0.4338
Clostridium beijerinckii	Clostridium	0.3986
Klebsiella variicola	Klebsiella	0.3973
Romboutsia sedimentorum	Romboutsia	0.3341
Clostridium estertheticum	Clostridium	0.2746
Romboutsia timonensis	Romboutsia	0.2737
Citrobacter amalonaticus	Citrobacter	0.2535
Roseateles puraquae	Roseateles	0.2347

Saved public metadata

{
  "run_accession": "SRR28257770",
  "study_accession": "PRJNA1083214",
  "sample_accession": "SAMN40240919",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "1026339",
  "base_count": "1588263629",
  "fastq_bytes": "1484882482",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/070/SRR28257770/SRR28257770_1.fastq.gz",
  "sample_title": "",
  "scientific_name": "gut metagenome"
}

Public files

SRR28257770_1.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": "31f6d1b528041dd7fc5fed7f3c9a299a462c51164427bf1ded3da7ffa4e83370",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1587.0,
  "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": 20000,
    "reads_skipped": 8644,
    "elapsed_seconds": 4.720737491000001,
    "reads_submitted": 20000,
    "reads_after_filter": 20000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 33,
      "fraction": 0.165,
      "adapters_found": {
        "27F": 32,
        "BC_FLANK": 1
      },
      "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."
}