ERR7746094_bin.246
uncultured Streptococcus sp.
This sample represents an uncultured Streptococcus sp. MAG assembled and binned from ERR7746094.
16S rRNAs recovered
0
16S recovered
FALSE
16S recovery software
barrnap;0.9;--kingdom bac
23S rRNAs recovered
0
5S rRNAs recovered
0
CheckM strain heterogeneity
61.54
ENA first public
2022-04-01
ENA last update
2022-04-01
External Id
SAMEA13520176
GTDB r202 classification
d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp001556435
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-04-01T08:28:10Z
INSDC last update
2022-04-01T08:28:10Z
INSDC status
public
MAG coverage depth
18.74
MAG coverage software
Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.
Submitter Id
REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_G_14_1102.246
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
binning parameters
Reads from ERR7746094 were assembled into contigs (ERZ4561846). The following read sets from this study were the most similar to ERR7746094 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746094,ERR7745588,ERR7746793,ERR7747255,ERR7746411,ERR7745953,ERR7747522,ERR7745582,ERR7738588,ERR7738556. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4561846. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.
binning software
MetaBAT2 v2.15; MAGpurify v2.1.0
collection date
2013-09-07
completeness approach
CheckM marker lineage: g__Streptococcus (UID684)
completeness score
91.46
completeness software
CheckM;1.1.2;lineage_wf
contamination score
1.57
contamination screening input
reads
contamination screening parameters
All reads in ERR7746094 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).
environment (biome)
terrestrial biome
environment (feature)
human-associated habitat
environment (material)
feces
geographic location (country and/or sea)
Tanzania
geographic location (elevation)
1287
geographic location (latitude)
-3.55
geographic location (longitude)
-34.58
inter-study species representative
GUT_GENOME089567
intra-study species representative
ERR7738600_bin.29
investigation type
metagenome-assembled genome
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
33
project name
Metagenome sequencing of Hadza gut microbiome
reassembly post binning
No
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
ERS2585526
sample name
REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_G_14_1102.246
sequencing method
Illumina NovaSeq 6000
tRNA extraction software
tRNAscan-SE;2.0.9;-B
taxonomic classification
GTDB-TK v1.7.0, r202 database, default parameters
taxonomic identity marker
multi-marker approach
unique standard tRNAs extracted
17