title: ERR7738606_virus.6080
organism: Siphoviridae environmental samples
description: This sample represents an uncultured Siphoviridae virus assembled from ERR7738606.
attributes.tag: BACPHLIP temperate score
attributes.value: 0.0125
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-12-27
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-12-27
attributes.tag: External Id
attributes.value: SAMEA13543187
attributes.tag: INSDC center alias
attributes.value: Stanford University School of Medicine
attributes.tag: INSDC center name
attributes.value: stanford university school of medicine
attributes.tag: INSDC first public
attributes.value: 2022-12-27T00:31:22Z
attributes.tag: INSDC last update
attributes.value: 2022-12-27T00:31:22Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: MAG coverage depth
attributes.value: 7.03788
attributes.tag: MAG coverage software
attributes.value: Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.
attributes.tag: Number of BLAST hits supporting host taxonomy
attributes.value: 1
attributes.tag: Number of CRISPR spacer hits supporting host taxonomy
attributes.value: 16
attributes.tag: Submitter Id
attributes.value: Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_6080_length_19236_cov_3.806149
attributes.tag: Viral contig found in MAG
attributes.value: ERR7738606_bin.315
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.
attributes.tag: assembly software
attributes.value: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz
attributes.tag: collection_date
attributes.value: 2014-04-05
attributes.tag: completeness approach
attributes.value: CheckV; AAI-based (high-confidence)
attributes.tag: completeness score
attributes.value: 51.15
attributes.tag: completeness software
attributes.value: CheckV;0.8.1;end-to-end, database v1.0
attributes.tag: detection type
attributes.value: independent sequence (UViG)
attributes.tag: environment (biome)
attributes.value: terrestrial biome
attributes.tag: environment (feature)
attributes.value: human-associated habitat
attributes.tag: environment (material)
attributes.value: feces
attributes.tag: feature prediction
attributes.value: Prodigal;2.6.3;meta
attributes.tag: geographic location (country and/or sea)
attributes.value: Tanzania
attributes.tag: geographic location (elevation)
attributes.value: 1287
attributes.tag: geographic location (latitude)
attributes.value: -3.55
attributes.tag: geographic location (longitude)
attributes.value: -34.58
attributes.tag: host prediction approach
attributes.value: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).
attributes.tag: investigation type
attributes.value: uncultivated viral genomes
attributes.tag: isolation_source
attributes.value: human feces
attributes.tag: metagenomic source
attributes.value: human gut metagenome
attributes.tag: nucleic acid extraction
attributes.value: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
attributes.tag: number of standard tRNAs extracted
attributes.value: NA
attributes.tag: number of unique standard tRNAs extracted
attributes.value: NA
attributes.tag: percent of BLAST hits supporting viral taxonomy
attributes.value: 0.9230769230769232
attributes.tag: predicted genome structure
attributes.value: non-segmented
attributes.tag: predicted genome type
attributes.value: dsDNA
attributes.tag: project name
attributes.value: Human gut UViGs
attributes.tag: reference database(s)
attributes.value: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)
attributes.tag: reference for biomaterial
attributes.value: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
attributes.tag: sample collection device or method
attributes.value: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
attributes.tag: sample derived from
attributes.value: ERS2585895
attributes.tag: sample name
attributes.value: Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_6080_length_19236_cov_3.806149
attributes.tag: sequencing method
attributes.value: Illumina NovaSeq 6000
attributes.tag: similarity search method
attributes.value: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5
attributes.tag: source of UViGs
attributes.value: metagenome (not viral targeted)
attributes.tag: species-level group of predicted host
attributes.value: NA
attributes.tag: tRNA extraction software
attributes.value: tRNAscan-SE;2.0.9;-B
attributes.tag: taxonomic classification
attributes.value: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.
attributes.tag: taxonomy of predicted host
attributes.value: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk
attributes.tag: vOTU classification approach
attributes.value: 95% ANI;85% AF;greedy, centroid-based
attributes.tag: vOTU database
attributes.value: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0
attributes.tag: vOTU representative
attributes.value: ERR7746345_virus.1821
attributes.tag: vOTU sequence comparison approach
attributes.value: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90
attributes.tag: viral identification software
attributes.value: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults
attributes.tag: viral taxonomy
attributes.value: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae
attributes.tag: virus enrichment approach
attributes.value: none