ERR7738957_virus.128
Myoviridae environmental samples
BACPHLIP temperate score
0.03997797356828193
ENA-FIRST-PUBLIC
2022-12-27
ENA-LAST-UPDATE
2022-12-27
External Id
SAMEA13531635
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-12-27T01:24:45Z
INSDC last update
2022-12-27T01:24:45Z
INSDC status
public
MAG coverage depth
176.181
MAG coverage software
Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) 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
NA
Number of CRISPR spacer hits supporting host taxonomy
NA
Submitter Id
Hadza_MoBio_hadza-A-D_F_2_1628__NODE_128_length_172915_cov_110.630428
Viral contig found in MAG
NA
assembly quality
Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.
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
2014-02-01
completeness approach
CheckV; DTR (high-confidence)
completeness score
100
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
3
number of unique standard tRNAs extracted
3
percent of BLAST hits supporting viral taxonomy
0.5
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
ERS2585872
sample name
Hadza_MoBio_hadza-A-D_F_2_1628__NODE_128_length_172915_cov_110.630428
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
NA
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
ERR7738957_virus.128
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; Myoviridae
virus enrichment approach
none