SRR28257762 · Gut microbiome

SRR28257762

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 (%)
Serratia marcescens	Serratia	38.0728
Enterobacter hormaechei	Enterobacter	13.9784
Serratia surfactantfaciens	Serratia	10.9587
Enterococcus faecium	Enterococcus	8.7452
Serratia rubidaea	Serratia	6.7011
Enterobacter roggenkampii	Enterobacter	3.5346
Pseudocitrobacter faecalis	Pseudocitrobacter	3.3540
Enterococcus faecalis	Enterococcus	1.6945
Serratia plymuthica	Serratia	1.6537
Enterococcus avium	Enterococcus	1.3323
Lactococcus lactis	Lactococcus	1.0945
Lactococcus garvieae	Lactococcus	1.0337
Enterobacter asburiae	Enterobacter	0.9517
Serratia ficaria	Serratia	0.8765
Enterococcus columbae	Enterococcus	0.7983
Enterobacter cloacae	Enterobacter	0.7572
Serratia nematodiphila	Serratia	0.5943
Serratia odorifera	Serratia	0.5886
Enterobacter kobei	Enterobacter	0.5649
Enterococcus hirae	Enterococcus	0.5454
Serratia fonticola	Serratia	0.4954
Fructilactobacillus sanfranciscensis	Fructilactobacillus	0.4543
Lacticaseibacillus paracasei	Lacticaseibacillus	0.3826
Staphylococcus aureus	Staphylococcus	0.3228
Enterobacter ludwigii	Enterobacter	0.2734
Enterobacter soli	Enterobacter	0.2409

Saved public metadata

{
  "run_accession": "SRR28257762",
  "study_accession": "PRJNA1083214",
  "sample_accession": "SAMN40240927",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "58092",
  "base_count": "88299075",
  "fastq_bytes": "81735570",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/062/SRR28257762/SRR28257762_1.fastq.gz",
  "sample_title": "",
  "scientific_name": "gut metagenome"
}

Public files

SRR28257762_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": "b80b9d8b89d06210e0ec4ed41540f8b0c1e2f9b3978632b9cbab17436e785d7a",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1558.0,
  "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": 11602,
    "elapsed_seconds": 1.5217370300006223,
    "reads_submitted": 20000,
    "reads_after_filter": 20000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 31,
      "fraction": 0.155,
      "adapters_found": {
        "27F": 29,
        "BC_FLANK": 2
      },
      "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."
}