SRR28267103 · 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 | 28.2850 |
| Neisseria lactamica | Neisseria | 24.1505 |
| Neisseria animalis | Neisseria | 12.4971 |
| Neisseria polysaccharea | Neisseria | 11.3434 |
| Neisseria meningitidis | Neisseria | 4.9170 |
| Neisseria subflava | Neisseria | 4.2609 |
| Tessaracoccus aquimaris | Tessaracoccus | 1.2909 |
| Tessaracoccus flavus | Tessaracoccus | 1.1745 |
| Enterococcus faecium | Enterococcus | 1.0545 |
| Chryseobacterium indologenes | Chryseobacterium | 0.8610 |
| Bacteroides timonensis | Bacteroides | 0.8035 |
| Kocuria varians | Kocuria | 0.6383 |
| Parabacteroides merdae | Parabacteroides | 0.5901 |
| Neisseria zalophi | Neisseria | 0.5376 |
| Propioniciclava sinopodophylli | Propioniciclava | 0.5059 |
| Paracoccus kondratievae | Paracoccus | 0.4911 |
| Kocuria rosea | Kocuria | 0.4876 |
| Ruminococcus champanellensis | Ruminococcus | 0.4804 |
| Paracoccus aestuarii | Paracoccus | 0.4783 |
| Dietzia maris | Dietzia | 0.4757 |
| Tessaracoccus profundi | Tessaracoccus | 0.4697 |
| Alistipes inops | Alistipes | 0.4094 |
| Neisseria arctica | Neisseria | 0.3866 |
| Lactococcus garvieae | Lactococcus | 0.3733 |
| Neisseria gonorrhoeae | Neisseria | 0.3347 |
| Neisseria animaloris | Neisseria | 0.3225 |
| Tessaracoccus lubricantis | Tessaracoccus | 0.3027 |
| Ruminococcus callidus | Ruminococcus | 0.2783 |
| Citrobacter freundii | Citrobacter | 0.2469 |
| Gallicola barnesae | Gallicola | 0.2288 |
| Tessaracoccus flavescens | Tessaracoccus | 0.2123 |
| Neisseria elongata | Neisseria | 0.1879 |
| Granulicatella balaenopterae | Granulicatella | 0.1867 |
| Neisseria dumasiana | Neisseria | 0.1563 |
| Bacteroides stercoris | Bacteroides | 0.1539 |
| Enterococcus alcedinis | Enterococcus | 0.1437 |
| Bradyrhizobium elkanii | Bradyrhizobium | 0.1325 |
| Lactobacillus delbrueckii | Lactobacillus | 0.0843 |
| Gemmata obscuriglobus | Gemmata | 0.0662 |
Saved public metadata
{
"run_accession": "SRR28267103",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210550",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "54011",
"base_count": "89335369",
"fastq_bytes": "66051523",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/003/SRR28267103/SRR28267103_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": "fc66e010617b6b35796bceb9af06f64d94826e9fa1562652b13c0a8762cfa57b",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1661.0,
"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": 3272,
"elapsed_seconds": 1.8267002350003168,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 106,
"fraction": 0.53,
"adapters_found": {
"BC_FLANK": 12,
"RAP": 92,
"27F": 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."
}