SRR28257754 · Gut microbiome
SRR28257754
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 (%) |
|---|---|---|
| Weissella cibaria | Weissella | 17.3082 |
| Leuconostoc lactis | Leuconostoc | 12.4313 |
| Leuconostoc mesenteroides | Leuconostoc | 11.8242 |
| Leuconostoc carnosum | Leuconostoc | 9.4850 |
| Weissella ceti | Weissella | 8.0642 |
| Weissella kandleri | Weissella | 6.1066 |
| Fructobacillus pseudoficulneus | Fructobacillus | 5.3004 |
| Weissella viridescens | Weissella | 4.5662 |
| Streptococcus salivarius | Streptococcus | 3.5744 |
| Leuconostoc pseudomesenteroides | Leuconostoc | 2.9648 |
| Streptococcus downei | Streptococcus | 1.6357 |
| Fructobacillus tropaeoli | Fructobacillus | 1.5286 |
| Leuconostoc gelidum | Leuconostoc | 1.5213 |
| Weissella thailandensis | Weissella | 1.4633 |
| Leuconostoc citreum | Leuconostoc | 1.3691 |
| Weissella hellenica | Weissella | 1.2317 |
| Weissella confusa | Weissella | 1.0991 |
| Streptococcus anginosus | Streptococcus | 0.9262 |
| Streptococcus gordonii | Streptococcus | 0.8819 |
| Streptococcus pyogenes | Streptococcus | 0.8015 |
| Leuconostoc kimchii | Leuconostoc | 0.6400 |
| Fructobacillus ficulneus | Fructobacillus | 0.5545 |
| Weissella koreensis | Weissella | 0.5153 |
| Fructobacillus fructosus | Fructobacillus | 0.4856 |
| Streptococcus sanguinis | Streptococcus | 0.4597 |
| Leuconostoc garlicum | Leuconostoc | 0.4593 |
| Weissella soli | Weissella | 0.4047 |
| Streptococcus mitis | Streptococcus | 0.3901 |
| Streptococcus pneumoniae | Streptococcus | 0.3774 |
| Fructobacillus durionis | Fructobacillus | 0.3504 |
| Leuconostoc palmae | Leuconostoc | 0.3216 |
| Streptococcus dysgalactiae | Streptococcus | 0.3208 |
| Leuconostoc fallax | Leuconostoc | 0.2068 |
| Streptococcus cristatus | Streptococcus | 0.1731 |
| Weissella paramesenteroides | Weissella | 0.1436 |
| Leuconostoc miyukkimchii | Leuconostoc | 0.1137 |
Saved public metadata
{
"run_accession": "SRR28257754",
"study_accession": "PRJNA1083214",
"sample_accession": "SAMN40240934",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "302189",
"base_count": "460975497",
"fastq_bytes": "431807930",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/054/SRR28257754/SRR28257754_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": "1f6382d2ca27c785a63952786c8efc95201c4b029d6acabb41564febf68bb4ca",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1574.0,
"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": 1440,
"elapsed_seconds": 1.9363493430000744,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 39,
"fraction": 0.195,
"adapters_found": {
"27F": 39
},
"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."
}