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 (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) 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_E_2_1148__NODE_2208_length_20334_cov_9.507183

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 (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 ERR7738254.

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: 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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

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__Gemmiger;unk;unk

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

characteristic: vOTU representative

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


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_MoBio_hadza-A-D_E_2_1148__NODE_29_length_213968_cov_17.452553

tag: Namespace:Stanford University School of Medicine

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: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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

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 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: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835

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: 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: 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 (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) 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_E_2_1148__NODE_412_length_61331_cov_4.723969

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

text: This sample represents an uncultured Caudovirales virus assembled from ERR7738254.

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)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;unk;unk;unk

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

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

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: Hadza_MoBio_hadza-A-D_E_2_1148__NODE_505_length_54846_cov_8.760448

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 ERR7738254.

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 (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).

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 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__Firmicutes_A;unk;unk;unk;unk;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: SRA accession

text: Hadza_MoBio_hadza-A-D_E_2_1148__NODE_652_length_47413_cov_36.239015

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 (medium-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

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

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: SRA accession

text: Hadza_MoBio_hadza-A-D_E_2_1148__NODE_762_length_42710_cov_7.202332

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

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 (longitude)

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 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

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

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

text: Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) 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_E_2_1148__NODE_847_length_39658_cov_13.125894

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 Caudovirales virus assembled from ERR7738254.

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)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

text: uncultured Caudovirales phage

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__Dysosmobacter;s__Dysosmobacter sp001916835

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


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 (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) 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-I-L_N_11_1304__NODE_142_length_107450_cov_62.617883_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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 provirus assembled from ERR7738256.

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 (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).

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 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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis

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_MoBio_hadza-I-L_N_11_1304__NODE_32_length_202134_cov_239.666995_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

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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)

characteristic: reference database(s)

text: Siphoviridae environmental samples

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__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis

characteristic: taxonomy of predicted host

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

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-I-L_N_11_1304__NODE_469_length_56728_cov_375.450760_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

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial 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 (longitude)

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 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

characteristic: taxonomic classification

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

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

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-I-L_N_11_1304__NODE_1206_length_31815_cov_3.600447

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 Siphoviridae virus assembled from ERR7738256.

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: 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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-917;g__CAG-475;s__CAG-475 sp900550855

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

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


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 (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) 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-I-L_N_11_1304__NODE_162_length_100189_cov_7.287708

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

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

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).

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 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__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

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

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-I-L_N_11_1304__NODE_320_length_71516_cov_7.645166

characteristic: Submitter Id

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; 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)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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)

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

characteristic: taxonomy of predicted host

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

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: SRA accession

text: Hadza_MoBio_hadza-I-L_N_11_1304__NODE_497_length_54632_cov_8.459408

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 (medium-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

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

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 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

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

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

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

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_MoBio_hadza-I-L_N_11_1304__NODE_714_length_44361_cov_47.965789

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 Caudovirales virus assembled from ERR7738256.

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 (elevation)

characteristic: geographic location (latitude)

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: 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

characteristic: reference database(s)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

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

text: Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) 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_M_18_1188__NODE_163_length_98708_cov_61.270959_1

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 (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 ERR7738257.

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 (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).

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 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: 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


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-A-D_M_18_1188__NODE_510_length_54629_cov_19.740321_1

characteristic: Submitter Id

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 ERR7738257.

characteristic: description

text: provirus (UpViG)

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: 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: 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)

characteristic: reference database(s)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035

characteristic: taxonomy of predicted host

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

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-A-D_M_18_1188__NODE_90_length_127857_cov_25.344146_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 (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (longitude)

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 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

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

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 (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) 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_M_18_1188__NODE_1411_length_29492_cov_131.153629

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 Caudovirales virus assembled from ERR7738257.

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: 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

characteristic: reference database(s)

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

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: viral identification software

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: Hadza_MoBio_hadza-A-D_M_18_1188__NODE_162_length_98763_cov_8.224257

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; 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 crAssphage cr8_1 virus assembled from ERR7738257.

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)

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).

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: uncultured podovirus

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured podovirus

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

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; Podoviridae; crAss-like viruses; crAssphage cr8_1


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-A-D_M_18_1188__NODE_405_length_61404_cov_7.804556

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 (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 ERR7738257.

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 (latitude)

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)

characteristic: reference database(s)

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.

characteristic: taxonomy of predicted host

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

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 (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) 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_M_18_1188__NODE_727_length_45690_cov_5.326113

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)

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (longitude)

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 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

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

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_M_18_1188__NODE_8235_length_6996_cov_3.463795

characteristic: Submitter Id

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 (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 ERR7738257.

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 (latitude)

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

characteristic: reference database(s)

text: uncultured podovirus

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 sp900551275

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

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 (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) 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_H_5_THA1064JZ__NODE_111_length_137426_cov_7.576102_1

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 (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 ERR7738258.

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: Nepal

characteristic: geographic location (elevation)

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).

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 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__Angelakisella;s__Angelakisella sp900547385

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

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


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_H_5_THA1064JZ__NODE_712_length_46178_cov_4.487712_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 Myoviridae provirus assembled from ERR7738258.

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: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

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__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia;s__Serratia marcescens_K

characteristic: taxonomy of predicted host

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

characteristic: vOTU representative

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: Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_1492_length_24405_cov_4.417914

characteristic: Submitter Id

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 virus assembled from ERR7738258.

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: Nepal

characteristic: geographic location (elevation)

characteristic: geographic location (longitude)

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 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

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;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

characteristic: viral identification software

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

text: Reads (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) 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_H_5_THA1064JZ__NODE_501_length_59839_cov_10.931880

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 Podoviridae virus assembled from ERR7738258.

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 (country and/or sea)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus;s__Duodenibacillus massiliensis

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: 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: Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_777_length_43434_cov_13.248380

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 (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 Taranis virus assembled from ERR7738258.

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: Nepal

characteristic: geographic location (elevation)

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).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Myoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

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

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

characteristic: taxonomic classification

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

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; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis


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 (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) 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_M_13_1797__NODE_1147_length_31760_cov_12.272354_1

characteristic: Submitter Id

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 Bacteroides phage F2 provirus assembled from ERR7738259.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975

characteristic: taxonomy of predicted host

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: 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_M_13_1797__NODE_801_length_40030_cov_43.569820_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 Siphoviridae provirus assembled from ERR7738259.

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 (elevation)

characteristic: geographic location (longitude)

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 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__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705

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: 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: SRA accession

text: Hadza_MoBio_hadza-E-H_M_13_1797__NODE_1683_length_24088_cov_6.530007

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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 (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 virus assembled from ERR7738259.

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 (latitude)

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 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)

characteristic: reference database(s)

text: uncultured Caudovirales phage

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

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

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 (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) 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_M_13_1797__NODE_357_length_65207_cov_57.188746

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; 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 ERR7738259.

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 (elevation)

characteristic: geographic location (longitude)

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

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 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__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995

characteristic: taxonomy of predicted host

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

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


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_M_13_1797__NODE_525_length_51756_cov_6.912053

characteristic: Submitter Id

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

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)

characteristic: geographic location (latitude)

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900546445

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

characteristic: vOTU sequence comparison approach