SRR28267196 · 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 (%) |
|---|---|---|
| Chryseobacterium indologenes | Chryseobacterium | 20.3943 |
| Snodgrassella alvi | Snodgrassella | 14.7042 |
| Kocuria varians | Kocuria | 9.9050 |
| Campylobacter sputorum | Campylobacter | 8.6955 |
| Kocuria rosea | Kocuria | 7.0749 |
| Gallicola barnesae | Gallicola | 5.0524 |
| Niabella drilacis | Niabella | 3.8276 |
| Arcobacter trophiarum | Arcobacter | 3.0427 |
| Lysobacter panacisoli | Lysobacter | 2.9295 |
| Niabella soli | Niabella | 2.6991 |
| Niabella yanshanensis | Niabella | 2.3864 |
| Corynebacterium bovis | Corynebacterium | 1.9594 |
| Paracoccus kondratievae | Paracoccus | 1.4286 |
| Paracoccus aestuarii | Paracoccus | 1.3206 |
| Campylobacter curvus | Campylobacter | 1.2394 |
| Niabella tibetensis | Niabella | 1.0579 |
| Allofrancisella guangzhouensis | Allofrancisella | 0.9765 |
| Corynebacterium matruchotii | Corynebacterium | 0.9386 |
| Nocardioides marmoraquaticus | Nocardioides | 0.9341 |
| Ralstonia syzygii | Ralstonia | 0.8402 |
| Ralstonia pseudosolanacearum | Ralstonia | 0.8368 |
| Tessaracoccus aquimaris | Tessaracoccus | 0.8184 |
| Paracoccus chinensis | Paracoccus | 0.8147 |
| Corynebacterium ammoniagenes | Corynebacterium | 0.6575 |
| Niabella hirudinis | Niabella | 0.6573 |
| Sphingomonas paucimobilis | Sphingomonas | 0.6085 |
| Kocuria indica | Kocuria | 0.5940 |
| Chryseobacterium jeonii | Chryseobacterium | 0.5369 |
| Propioniciclava sinopodophylli | Propioniciclava | 0.5174 |
| Tessaracoccus flavus | Tessaracoccus | 0.5009 |
| Paracoccus hibisci | Paracoccus | 0.4837 |
| Tessaracoccus lubricantis | Tessaracoccus | 0.4485 |
| Ralstonia pickettii | Ralstonia | 0.4108 |
| Sphingopyxis terrae | Sphingopyxis | 0.3963 |
| Spirosoma spitsbergense | Spirosoma | 0.3114 |
Saved public metadata
{
"run_accession": "SRR28267196",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210583",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "259187",
"base_count": "426209632",
"fastq_bytes": "359649133",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/096/SRR28267196/SRR28267196_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": "daba4c857ab8fb1ddddb1b55207f2ee3d47511e40a98369f95492f0c0b83df5f",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1650.0,
"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": 12769,
"elapsed_seconds": 1.4584439089999819,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 121,
"fraction": 0.605,
"adapters_found": {
"RAP": 100,
"BC_FLANK": 21
},
"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."
}