SRR28629909 · Gut microbiome
SRR28629909
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 (%) |
|---|---|---|
| Polaribacter sejongensis | Polaribacter | 19.9207 |
| Mycoplasma iguanae | Mycoplasma | 11.5258 |
| Helicobacter pullorum | Helicobacter | 10.8604 |
| Helicobacter pylori | Helicobacter | 7.9575 |
| Helicobacter salomonis | Helicobacter | 4.4453 |
| Methylobacterium oryzae | Methylobacterium | 4.2118 |
| Methylobacterium radiotolerans | Methylobacterium | 4.0588 |
| Methylobacterium phyllosphaerae | Methylobacterium | 3.8970 |
| Ralstonia solanacearum | Ralstonia | 2.4410 |
| Helicobacter cetorum | Helicobacter | 2.3646 |
| Methylobacterium bullatum | Methylobacterium | 1.9378 |
| Streptococcus salivarius | Streptococcus | 1.8836 |
| Helicobacter rodentium | Helicobacter | 1.8596 |
| Methylobacterium gregans | Methylobacterium | 1.7815 |
| Streptococcus anginosus | Streptococcus | 1.4583 |
| Polaribacter lacunae | Polaribacter | 1.4433 |
| Polaribacter reichenbachii | Polaribacter | 1.3692 |
| Ralstonia pseudosolanacearum | Ralstonia | 1.3635 |
| Roseateles depolymerans | Roseateles | 1.3600 |
| Roseateles puraquae | Roseateles | 1.3385 |
| Helicobacter muridarum | Helicobacter | 1.2981 |
| Cutibacterium acnes | Cutibacterium | 1.2837 |
| Methylobacterium marchantiae | Methylobacterium | 0.9623 |
| Sphingomonas paucimobilis | Sphingomonas | 0.9431 |
| Methylobacterium aerolatum | Methylobacterium | 0.9396 |
| Streptococcus downei | Streptococcus | 0.9041 |
| Helicobacter valdiviensis | Helicobacter | 0.8942 |
| Methylobacterium terrae | Methylobacterium | 0.8908 |
| Ralstonia insidiosa | Ralstonia | 0.8456 |
| Helicobacter hepaticus | Helicobacter | 0.7540 |
| Mycoplasma crocodyli | Mycoplasma | 0.6667 |
| Mycoplasma suis | Mycoplasma | 0.6241 |
| Ralstonia pickettii | Ralstonia | 0.5635 |
| Polaribacter porphyrae | Polaribacter | 0.5592 |
| Sphingomonas yantingensis | Sphingomonas | 0.3930 |
Saved public metadata
{
"run_accession": "SRR28629909",
"study_accession": "PRJNA1099261",
"sample_accession": "SAMN40934552",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "265774",
"base_count": "80206109",
"fastq_bytes": "79623887",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR286/009/SRR28629909/SRR28629909_1.fastq.gz",
"sample_title": "",
"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": "55a26ada3e9d93221e6ca2cd20d4810e1a200de5e086b1ec875dccc7467cd58e",
"length_window_bp": [
1200,
2000
],
"median_read_length": 234.0,
"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": 16059,
"elapsed_seconds": 1.2684777169997687,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 81,
"fraction": 0.405,
"adapters_found": {
"1492R_rc": 32,
"27F": 49
},
"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."
}