ERR7745835_virus.257
uncultured podovirus
BACPHLIP temperate score
0.10576727073640042
ENA-FIRST-PUBLIC
2022-12-27
ENA-LAST-UPDATE
2022-12-27
External Id
SAMEA13532218
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-12-27T01:24:34Z
INSDC last update
2022-12-27T01:24:34Z
INSDC status
public
MAG coverage depth
13.3802
MAG coverage software
Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.
Number of BLAST hits supporting host taxonomy
0
Number of CRISPR spacer hits supporting host taxonomy
25
Submitter Id
Hadza_MoBio_hadza-E-H_E_9_1723__NODE_257_length_113850_cov_7.861435
Viral contig found in MAG
NA
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics.
assembly software
metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz
collection_date
2014-05-07
completeness approach
CheckV; AAI-based (high-confidence)
completeness score
61.17
completeness software
CheckV;0.8.1;end-to-end, database v1.0
detection type
independent sequence (UViG)
environment (biome)
terrestrial biome
environment (feature)
human-associated habitat
environment (material)
feces
feature prediction
Prodigal;2.6.3;meta
geographic location (country and/or sea)
Tanzania
geographic location (elevation)
1287
geographic location (latitude)
-3.55
geographic location (longitude)
-34.58
host prediction approach
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).
investigation type
uncultivated viral genomes
isolation_source
human feces
metagenomic source
human gut metagenome
nucleic acid extraction
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
number of standard tRNAs extracted
17
number of unique standard tRNAs extracted
15
percent of BLAST hits supporting viral taxonomy
0.5172413793103449
predicted genome structure
non-segmented
predicted genome type
dsDNA
project name
Human gut UViGs
reference database(s)
NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)
reference for biomaterial
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
sample collection device or method
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
sample derived from
ERS2585966
sample name
Hadza_MoBio_hadza-E-H_E_9_1723__NODE_257_length_113850_cov_7.861435
sequencing method
Illumina NovaSeq 6000
similarity search method
diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5
source of UViGs
metagenome (not viral targeted)
species-level group of predicted host
NA
tRNA extraction software
tRNAscan-SE;2.0.9;-B
taxonomic classification
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.
taxonomy of predicted host
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk
vOTU classification approach
95% ANI;85% AF;greedy, centroid-based
vOTU database
MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0
vOTU representative
ERR7747322_virus.71
vOTU sequence comparison approach
blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90
viral identification software
CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults
viral taxonomy
Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses
virus enrichment approach
none