SRR28629912 · Gut microbiome

SRR28629912

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 (%)
Roseateles depolymerans	Roseateles	27.8782
Ralstonia solanacearum	Ralstonia	15.3163
Roseateles puraquae	Roseateles	8.7241
Roseateles chitosanitabidus	Roseateles	4.6410
Ralstonia insidiosa	Ralstonia	4.4582
Ralstonia pickettii	Ralstonia	3.9611
Roseateles saccharophilus	Roseateles	3.3926
Streptococcus salivarius	Streptococcus	2.5696
Ralstonia pseudosolanacearum	Ralstonia	2.4221
Methylobacterium oryzae	Methylobacterium	2.1644
Methylobacterium radiotolerans	Methylobacterium	1.9333
Sphingomonas melonis	Sphingomonas	1.6064
Methylobacterium phyllosphaerae	Methylobacterium	1.6041
Campylobacter jejuni	Campylobacter	1.4362
Ralstonia syzygii	Ralstonia	1.3278
Campylobacter lari	Campylobacter	1.2385
Roseateles aquatilis	Roseateles	1.0516
Staphylococcus aureus	Staphylococcus	1.0094
Methylobacterium bullatum	Methylobacterium	0.9937
Streptococcus anginosus	Streptococcus	0.9139
Sphingomonas paucimobilis	Sphingomonas	0.8305
Sphingomonas yantingensis	Sphingomonas	0.7371
Polaribacter sejongensis	Polaribacter	0.7268
Streptococcus downei	Streptococcus	0.7114
Ralstonia mannitolilytica	Ralstonia	0.6528
Streptococcus mitis	Streptococcus	0.5853
Streptococcus pneumoniae	Streptococcus	0.5555
Staphylococcus epidermidis	Staphylococcus	0.5410
Streptococcus equinus	Streptococcus	0.4854
Caulobacter vibrioides	Caulobacter	0.4598
Roseateles toxinivorans	Roseateles	0.4576
Lactococcus lactis	Lactococcus	0.4483
Streptococcus pyogenes	Streptococcus	0.4377
Roseateles noduli	Roseateles	0.4365
Methylobacterium terrae	Methylobacterium	0.4123
Caulobacter mirabilis	Caulobacter	0.4044
Methylobacterium indicum	Methylobacterium	0.3742
Caulobacter segnis	Caulobacter	0.3494
Streptococcus gordonii	Streptococcus	0.3438
Methylobacterium aerolatum	Methylobacterium	0.3408
Methylobacterium gregans	Methylobacterium	0.3360
Campylobacter sputorum	Campylobacter	0.2842
Lactococcus garvieae	Lactococcus	0.2427
Polaribacter reichenbachii	Polaribacter	0.2037

Saved public metadata

{
  "run_accession": "SRR28629912",
  "study_accession": "PRJNA1099261",
  "sample_accession": "SAMN40934549",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "MinION",
  "library_strategy": "AMPLICON",
  "library_source": "METAGENOMIC",
  "library_selection": "PCR",
  "read_count": "41811",
  "base_count": "37118444",
  "fastq_bytes": "34556646",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR286/012/SRR28629912/SRR28629912_1.fastq.gz",
  "sample_title": "",
  "scientific_name": "gut metagenome"
}

Public files

SRR28629912_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": "17af243d3a57c161e0007798c9ce370f60c43934ecd4b2624eadc62c43c8ee99",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1500.5,
  "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": 9208,
    "elapsed_seconds": 1.5929759600003308,
    "reads_submitted": 20000,
    "reads_after_filter": 20000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 43,
      "fraction": 0.215,
      "adapters_found": {
        "27F": 43
      },
      "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."
}