U-C
BioSample: SAMN22483465 · Study: PRJNA773113 · Body site: saliva
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 |
|---|---|---|---|
| Streptococcus salivarius | Streptococcus | Bacillota | 23.83716% |
| Streptococcus anginosus | Streptococcus | Bacillota | 21.28852% |
| Limosilactobacillus fermentum | Limosilactobacillus | Bacillota | 9.91416% |
| Streptococcus oralis | Streptococcus | Bacillota | 4.75915% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 4.20962% |
| Streptococcus downei | Streptococcus | Bacillota | 3.76788% |
| Streptococcus gordonii | Streptococcus | Bacillota | 3.27384% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 2.37620% |
| Lactobacillus delbrueckii | Lactobacillus | Bacillota | 2.09096% |
| Veillonella parvula | Veillonella | Bacillota | 2.07129% |
| Streptococcus mitis | Streptococcus | Bacillota | 1.97882% |
| Veillonella dispar | Veillonella | Bacillota | 1.58411% |
| Veillonella rodentium | Veillonella | Bacillota | 1.51446% |
| Limosilactobacillus oris | Limosilactobacillus | Bacillota | 1.47092% |
| Streptococcus pyogenes | Streptococcus | Bacillota | 1.22946% |
| Streptococcus mutans | Streptococcus | Bacillota | 1.05510% |
| Granulicatella balaenopterae | Granulicatella | Bacillota | 0.91177% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 0.89875% |
| Streptococcus cristatus | Streptococcus | Bacillota | 0.88077% |
| Gemella palaticanis | Gemella | Bacillota | 0.87582% |
| Limosilactobacillus mucosae | Limosilactobacillus | Bacillota | 0.83136% |
| Streptococcus periodonticum | Streptococcus | Bacillota | 0.80675% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.75430% |
| Streptococcus pluranimalium | Streptococcus | Bacillota | 0.54456% |
| Lactobacillus psittaci | Lactobacillus | Bacillota | 0.54364% |
| Streptococcus intermedius | Streptococcus | Bacillota | 0.49724% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 0.47033% |
| Gemella haemolysans | Gemella | Bacillota | 0.46314% |
| Streptococcus sinensis | Streptococcus | Bacillota | 0.39078% |
| Streptococcus equinus | Streptococcus | Bacillota | 0.37933% |
| Limosilactobacillus gorillae | Limosilactobacillus | Bacillota | 0.35853% |
| Gemella parahaemolysans | Gemella | Bacillota | 0.35071% |
| Streptococcus himalayensis | Streptococcus | Bacillota | 0.34526% |
| Limosilactobacillus reuteri | Limosilactobacillus | Bacillota | 0.31152% |
| Streptococcus marmotae | Streptococcus | Bacillota | 0.29919% |
| Veillonella seminalis | Veillonella | Bacillota | 0.25370% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.25279% |
| Streptococcus constellatus | Streptococcus | Bacillota | 0.24414% |
| Streptococcus vestibularis | Streptococcus | Bacillota | 0.24069% |
| Streptococcus dysgalactiae | Streptococcus | Bacillota | 0.20484% |
| Streptococcus acidominimus | Streptococcus | Bacillota | 0.16256% |
| Granulicatella elegans | Granulicatella | Bacillota | 0.15774% |
| Streptococcus halotolerans | Streptococcus | Bacillota | 0.13508% |
| Streptococcus suis | Streptococcus | Bacillota | 0.12960% |
| Streptococcus sobrinus | Streptococcus | Bacillota | 0.11692% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.11570% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 0.11314% |
| Gemella asaccharolytica | Gemella | Bacillota | 0.10993% |
| Streptococcus gallolyticus | Streptococcus | Bacillota | 0.10705% |
| Streptococcus alactolyticus | Streptococcus | Bacillota | 0.09387% |
| Streptococcus troglodytidis | Streptococcus | Bacillota | 0.08832% |
| Streptococcus ruminantium | Streptococcus | Bacillota | 0.08549% |
| Campylobacter concisus | Campylobacter | Pseudomonadota | 0.05303% |
53 of 53 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 |
|---|---|---|
| SRR16522314_1.fastq.gz | FASTQ / 346667150 | b18b403f76bf6c45e322be42024a3e83 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | bfe23cc2cfb713ab4e6f6355cfc781603937fc94e67c5b860251da79ace935da |
| median_read_length | 1604.0 |
| reads_in_length_window | 28535 |
| 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": 30000, "reads_skipped": 1635, "elapsed_seconds": 2.9778544449999345, "reads_submitted": 30000, "reads_after_filter": 30000, "adapter_scan": {"sampled": 200, "matched": 21, "fraction": 0.105, "adapters_found": {"27F": 21}, "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 | SRR16522314 |
|---|---|
| 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 | 377677957 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Not reported |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB10545744 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2021-08-20 |
| collection_date_end | 2021-08-20 |
| collection_date_start | 2021-08-19 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | USA: La Jolla |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | GridION sequencing: UA159 1:2 C |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | Not reported |
| environment_feature | Not reported |
| environment_material | Not reported |
| environmental_medium | Not reported |
| environmental_sample | Not reported |
| experiment_accession | SRX12725068 |
| experiment_alias | U-C |
| experiment_target | Not reported |
| experiment_title | GridION sequencing: UA159 1:2 C |
| 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/SRR165/014/SRR16522314/SRR16522314_1.fastq.gz |
| fastq_bytes | 346667150 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/014/SRR16522314/SRR16522314_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR165/014/SRR16522314/SRR16522314_1.fastq.gz |
| fastq_md5 | b18b403f76bf6c45e322be42024a3e83 |
| file_location | Not reported |
| first_created | 2021-10-23 |
| first_public | 2021-10-23 |
| 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 | saliva |
| last_updated | 2021-10-23 |
| lat | 32.87 |
| 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 | U-C |
| 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 | PCR |
| library_source | METAGENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Not reported |
| location | 32.87 N 117.24 W |
| location_end | 32.87 N 117.24 W |
| location_start | 32.87 N 117.24 W |
| lon | -117.24 |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Metagenome or environmental |
| 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 | 242779 |
| 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 | barcode17.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN22483465 |
| sample_alias | barcode17 |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | UA159 1:2 C |
| 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 | U-C |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS10674105 |
| secondary_study_accession | SRP342425 |
| 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 | Not reported |
| study_accession | PRJNA773113 |
| study_alias | PRJNA773113 |
| study_title | Tetramic acids mutanocyclin and reutericyclin-A, produced by Streptococcus mutans strain B04Sm5, modulate the ecology of an in vitro oral biofilm |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1314846 |
| 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 | barcode17 |
|---|---|
| title | U-C |
| description | UA159 1:2 C |
| collection_date | 2021-08-20 |
|---|---|
| INSDC secondary accession | SRS10674105 |
| NCBI submission package | Metagenome.environmental.1.0 |
| source_material_id | UA159 1:2 C |
| organism | human oral metagenome |
| host | Homo sapiens |
| geo_loc_name | USA: La Jolla |
| lat_lon | 32.87 N 117.24 W |
| isolation_source | saliva |
| BioSampleModel | Metagenome or environmental |
| ENA-FIRST-PUBLIC | 2021-10-21 |
| ENA-LAST-UPDATE | 2021-10-21 |
| run | SRR16522314 |
|---|---|
| sample | SAMN22483465 |
| study | PRJNA773113 |
| title | U-C |
| alias | barcode17 |
| site | saliva |
| 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 | 30000 |
| species_reported | 53 |
| human_primary | False |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.