SRR28267138 · Gut microbiome
Metagenome or environmental sample from gut metagenome
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 (%) |
|---|---|---|
| Neisseria dentiae | Neisseria | 27.6281 |
| Neisseria lactamica | Neisseria | 17.6946 |
| Neisseria polysaccharea | Neisseria | 11.2278 |
| Neisseria animalis | Neisseria | 8.6764 |
| Chryseobacterium indologenes | Chryseobacterium | 7.3177 |
| Neisseria subflava | Neisseria | 4.3646 |
| Pedobacter kyungheensis | Pedobacter | 3.1934 |
| Kocuria rosea | Kocuria | 3.1421 |
| Neisseria meningitidis | Neisseria | 3.1294 |
| Kocuria varians | Kocuria | 3.0846 |
| Gallicola barnesae | Gallicola | 1.0555 |
| Neisseria zalophi | Neisseria | 1.0033 |
| Tessaracoccus aquimaris | Tessaracoccus | 0.7539 |
| Pseudomonas aeruginosa | Pseudomonas | 0.6919 |
| Sphingobacterium multivorum | Sphingobacterium | 0.6657 |
| Niabella drilacis | Niabella | 0.5912 |
| Sphingobacterium thalpophilum | Sphingobacterium | 0.5740 |
| Propioniciclava sinopodophylli | Propioniciclava | 0.4790 |
| Paracoccus kondratievae | Paracoccus | 0.4435 |
| Niabella soli | Niabella | 0.4282 |
| Flavobacterium frigidimaris | Flavobacterium | 0.3772 |
| Flavobacterium columnare | Flavobacterium | 0.3768 |
| Neisseria gonorrhoeae | Neisseria | 0.3721 |
| Lysobacter panacisoli | Lysobacter | 0.3548 |
| Dietzia maris | Dietzia | 0.3371 |
| Niabella yanshanensis | Niabella | 0.3289 |
| Sphingobacterium spiritivorum | Sphingobacterium | 0.2756 |
| Sphingobacterium mizutaii | Sphingobacterium | 0.2495 |
| Kocuria indica | Kocuria | 0.2484 |
| Aeromonas veronii | Aeromonas | 0.2395 |
| Neisseria animaloris | Neisseria | 0.2147 |
| Snodgrassella alvi | Snodgrassella | 0.1877 |
| Sphingobium xenophagum | Sphingobium | 0.1685 |
| Dyadobacter jejuensis | Dyadobacter | 0.1242 |
Saved public metadata
{
"run_accession": "SRR28267138",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210589",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "368625",
"base_count": "607825731",
"fastq_bytes": "475627371",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/038/SRR28267138/SRR28267138_1.fastq.gz",
"sample_title": "Metagenome or environmental sample from gut metagenome",
"scientific_name": "gut metagenome"
}Public files
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": "feda8699634981a22bf1990e3f9893278c8c7feebf0f34a849950959e846c1a8",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1657.0,
"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": 8492,
"elapsed_seconds": 1.736993789999815,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 110,
"fraction": 0.55,
"adapters_found": {
"RAP": 92,
"BC_FLANK": 14,
"27F": 4
},
"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."
}