TP2CGP_1_ExVivo_plaque
BioSample: SAMN61250890 · Study: PRJNA1484659 · Body site: Oral Plaque
Interactive report · NCBI SRA · ENA
Relative abundance is normalized among reported taxa. No reported taxa does not establish absence of organisms.
| Species | Genus | Phylum | Abundance |
|---|---|---|---|
| Veillonella parvula | Veillonella | Bacillota | 19.34456% |
| Streptococcus gordonii | Streptococcus | Bacillota | 18.39884% |
| Streptococcus oralis | Streptococcus | Bacillota | 15.11085% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 9.79828% |
| Streptococcus cristatus | Streptococcus | Bacillota | 9.26560% |
| Streptococcus intermedius | Streptococcus | Bacillota | 5.84036% |
| Granulicatella elegans | Granulicatella | Bacillota | 4.41293% |
| Streptococcus anginosus | Streptococcus | Bacillota | 2.93363% |
| Gemella morbillorum | Gemella | Bacillota | 2.63926% |
| Streptococcus mitis | Streptococcus | Bacillota | 2.61782% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 2.33018% |
| Streptococcus salivarius | Streptococcus | Bacillota | 1.67797% |
| Veillonella dispar | Veillonella | Bacillota | 1.00149% |
| Aggregatibacter segnis | Aggregatibacter | Pseudomonadota | 1.00013% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.90289% |
| Abiotrophia defectiva | Abiotrophia | Bacillota | 0.85470% |
| Gemella haemolysans | Gemella | Bacillota | 0.69616% |
| Streptococcus milleri | Streptococcus | Bacillota | 0.64506% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.52928% |
19 of 19 reported species have an eligible reference. MAFFT alignment and FastTree GTR+CAT tree, pruned to this sample. This is not a phylogeny inferred from sample reads or ASVs. Root placement is arbitrary; branch lengths are substitutions per site.
Files contain the original full run. Downloads are hosted by ENA.
| File | Type / bytes | MD5 |
|---|---|---|
| SRR39418819_1.fastq.gz | FASTQ / 5270848 | 61c7c2680452c56df437a6e81f5c3e3c |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | a5cd37750505b2ee4b7ba59758bd3e7889160f4ff82da20b0faad99b87635f15 |
| median_read_length | 1470.0 |
| reads_in_length_window | 4117 |
| length_window_bp | [1200, 2000] |
| quality_scores | Unavailable in fetched FASTA; no measured quality filtering |
| classifier_stats | {"marker": "16s", "pipeline": "v18.8", "gpu": "RTX-PRO-6000", "input_path": "volume-fastq-gz", "reads_in": 4954, "reads_skipped": 98, "elapsed_seconds": 0.7249385340000174, "reads_submitted": 4954, "reads_after_filter": 4954, "adapter_scan": {"sampled": 200, "matched": 15, "fraction": 0.075, "adapters_found": {"BC_FLANK": 15}, "should_trim": true}, "porechop_ran": false, "porechop_reason": "fast-path: no adapter trimming required"} |
All retrieved values are included. Blank source values are displayed as “Not reported”. Expand the sections below to inspect the full record.
| run_accession | SRR39418819 |
|---|---|
| age | Not reported |
| aligned | Not reported |
| altitude | Not reported |
| assembly_quality | Not reported |
| assembly_software | Not reported |
| bam_aspera | Not reported |
| bam_bytes | Not reported |
| bam_file_role | Not reported |
| bam_ftp | Not reported |
| bam_galaxy | Not reported |
| bam_md5 | Not reported |
| base_count | 6713965 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Oral Cavity |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB16301393 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2026-04 |
| collection_date_end | 2026-04-30 |
| collection_date_start | 2026-03-31 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | USA |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | GridION sequencing: 16s Library of oral ex vivo plaque biofilm |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | Oral Cavity |
| environment_feature | Ex vivo culture |
| environment_material | Oral Plaque |
| environmental_medium | Oral Plaque |
| environmental_sample | Not reported |
| experiment_accession | SRX34135667 |
| experiment_alias | TP2CGP_1_mbio-R1 |
| experiment_target | Not reported |
| experiment_title | GridION sequencing: 16s Library of oral ex vivo plaque biofilm |
| experimental_factor | Not reported |
| experimental_protocol | Not reported |
| extraction_protocol | Not reported |
| faang_library_selection | Not reported |
| fastq_aspera | fasp.sra.ebi.ac.uk:/vol1/fastq/SRR394/019/SRR39418819/SRR39418819_1.fastq.gz |
| fastq_bytes | 5270848 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR394/019/SRR39418819/SRR39418819_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR394/019/SRR39418819/SRR39418819_1.fastq.gz |
| fastq_md5 | 61c7c2680452c56df437a6e81f5c3e3c |
| file_location | Not reported |
| first_created | 2026-07-05 |
| first_public | 2026-07-05 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Homo sapiens |
| host_body_site | Not reported |
| host_genotype | Not reported |
| host_gravidity | Not reported |
| host_growth_conditions | Not reported |
| host_phenotype | Not reported |
| host_scientific_name | Homo sapiens |
| host_sex | Not reported |
| host_status | Not reported |
| host_tax_id | 9606 |
| identified_by | Not reported |
| instrument_model | GridION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Not reported |
| last_updated | 2026-08-28 |
| lat | 37.54129 |
| library_construction_protocol | Not reported |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | TP2CGP_1_mbio-R1 |
| library_pcr_isolation_protocol | Not reported |
| library_prep_date | Not reported |
| library_prep_date_format | Not reported |
| library_prep_latitude | Not reported |
| library_prep_location | Not reported |
| library_prep_longitude | Not reported |
| library_selection | size fractionation |
| library_source | GENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Ex vivo culture |
| location | 37.54129 N 77.434769 W |
| location_end | 37.54129 N 77.434769 W |
| location_start | 37.54129 N 77.434769 W |
| lon | -77.434769 |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | MIMARKS.survey;MIGS/MIMS/MIMARKS.human-oral |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | Not reported |
| protocol_label | Not reported |
| read_count | 4954 |
| read_strand | Not reported |
| restriction_enzyme | Not reported |
| restriction_enzyme_target_sequence | Not reported |
| restriction_site | Not reported |
| rna_integrity_num | Not reported |
| rna_prep_3_protocol | Not reported |
| rna_prep_5_protocol | Not reported |
| rna_purity_230_ratio | Not reported |
| rna_purity_280_ratio | Not reported |
| rt_prep_protocol | Not reported |
| run_alias | TP2CGP_1_mbio-R1.fastq.gz |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN61250890 |
| sample_alias | TP2CGP_1_ExVivo_plaque |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | Sample-1 |
| sample_material | Not reported |
| sample_prep_interval | Not reported |
| sample_prep_interval_units | Not reported |
| sample_storage | Not reported |
| sample_storage_processing | Not reported |
| sample_title | Not reported |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS29751273 |
| secondary_study_accession | SRP714474 |
| sequencing_date | Not reported |
| sequencing_date_format | Not reported |
| sequencing_location | Not reported |
| sequencing_longitude | Not reported |
| sequencing_method | Not reported |
| sequencing_primer_catalog | Not reported |
| sequencing_primer_lot | Not reported |
| sequencing_primer_provider | Not reported |
| serotype | Not reported |
| serovar | Not reported |
| sex | Not reported |
| specimen_voucher | Not reported |
| sra_aspera | Not reported |
| sra_bytes | Not reported |
| sra_file_role | Not reported |
| sra_ftp | Not reported |
| sra_galaxy | Not reported |
| sra_md5 | Not reported |
| status | public |
| strain | multi-species |
| study_accession | PRJNA1484659 |
| study_alias | PRJNA1484659 |
| study_title | Ex Vivo Plaque biofilm 16s |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA2472700 |
| submission_tool | Not reported |
| submitted_aspera | Not reported |
| submitted_bytes | Not reported |
| submitted_file_role | Not reported |
| submitted_format | Not reported |
| submitted_ftp | Not reported |
| submitted_galaxy | Not reported |
| submitted_host_sex | Not reported |
| submitted_md5 | Not reported |
| submitted_read_type | Not reported |
| surveillance_target | Not reported |
| tag | env_geo;env_geo:terrestrial |
| target_gene | Not reported |
| tax_id | 447426 |
| tax_lineage | 1;2787823;12908;408169;410656;447426 |
| taxonomic_classification | Not reported |
| taxonomic_identity_marker | Not reported |
| temperature | Not reported |
| tissue_lib | Not reported |
| tissue_type | Not reported |
| transposase_protocol | Not reported |
| variety | Not reported |
| alias | TP2CGP_1_ExVivo_plaque |
|---|---|
| title | Not reported |
| description | Sample-1 |
| strain | multi-species |
|---|---|
| collection_date | 2026-04 |
| isol_growth_condt | Artificial Saliva |
| ref_biomaterial | Unpublished |
| organism | human oral metagenome |
| env_broad_scale | Oral Cavity |
| BioSampleModel | MIGS/MIMS/MIMARKS.human-oral |
| scientific_name | human oral metagenome |
| env_local_scale | Ex vivo culture |
| ENA-FIRST-PUBLIC | 2026-07-05 |
| ENA-LAST-UPDATE | 2026-09-08 |
| host | Homo sapiens |
| num_replicons | not applicable |
| geo_loc_name | USA |
| env_medium | Oral Plaque |
| lat_lon | 37.541290 N 77.434769 W |
| run | SRR39418819 |
|---|---|
| sample | SAMN61250890 |
| study | PRJNA1484659 |
| title | Not reported |
| alias | TP2CGP_1_ExVivo_plaque |
| site | Oral Plaque |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | True |
| state | complete |
| reads_input | 4954 |
| species_reported | 19 |
| human_primary | False |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.