characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_161_length_118324_cov_108.530897_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738531.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database


status: PUBLIC

tag: attribute

characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_298_length_94860_cov_28.359611_1

tag: Namespace:Stanford University School of Medicine

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: 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.

text: d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk

characteristic: taxonomy of predicted host

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_50_length_198969_cov_31.754314_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter;s__Fusicatenibacter saccharivorans

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_763_length_60467_cov_27.337821_1

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

characteristic: taxonomy of predicted host

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_12484_length_10926_cov_248.170062

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Salasmaviridae virus assembled from ERR7738531.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured Caudovirales phage

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae

characteristic: viral taxonomy


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1621_length_40505_cov_90.388617

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738531.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: 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.

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk

characteristic: taxonomy of predicted host

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1965_length_36595_cov_34.789638

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_2487_length_31880_cov_20.429928

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

characteristic: taxonomy of predicted host

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_3424_length_26396_cov_19.053497

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738531.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_4151_length_23430_cov_8.798570

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

characteristic: viral taxonomy


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_5212_length_20134_cov_26.466969

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

text: 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.

characteristic: taxonomic classification

text: d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_94_length_158870_cov_17.286234

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; HMM-based (lower-bound)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2407_length_29385_cov_206.576361_1

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738532.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_623_length_66303_cov_30.617537_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900542795

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1207_length_44861_cov_4.886008

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

text: 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.

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UMGS1603;s__UMGS1603 sp900553265

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1321_length_42881_cov_8.448369

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1529_length_39583_cov_5.262821

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Myoviridae virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: 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).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Myoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1776_length_36171_cov_7.362720

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1989_length_33439_cov_13.067742

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured Caudovirales phage

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

text: 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.

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2442_length_29047_cov_44.782499

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Podoviridae virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2819_length_26186_cov_165.120840

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_39_length_227802_cov_17.617271

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Myoviridae virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Myoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: 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.

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_447_length_77376_cov_11.455258

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: 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).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_5987_length_14482_cov_21.569524

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_G_3_1732__NODE_848_length_55428_cov_68.889397

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Lambdavirus virus assembled from ERR7738532.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_112_length_144865_cov_82.321525_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Faecalibacterium virus Lugh provirus assembled from ERR7738533.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: 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.

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_248_length_92848_cov_33.186481_1

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Caudovirales provirus assembled from ERR7738533.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Nepal

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured Caudovirales phage

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_677_length_51021_cov_400.588666_1

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738533.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Caudovirales phage

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_1865_length_24044_cov_5.788835

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics.

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Roseburia phage Jekyll virus assembled from ERR7738533.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Nepal

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured virus

text: non-segmented

text: uncharacterized

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured virus

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

characteristic: vOTU sequence comparison approach

text: Viruses; unclassified bacterial viruses; Roseburia phage Jekyll


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_595_length_56133_cov_13.058352

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738533.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Myoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: 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.

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_876_length_42660_cov_204.924712

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738533.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Nepal

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-A-D_B_3_1599__NODE_143_length_135997_cov_88.357880_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Caudovirales provirus assembled from ERR7738534.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Caudovirales phage

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales