ERR7745410_bin.83
uncultured Alphaproteobacteria bacterium
This sample represents an uncultured Alphaproteobacteria bacterium MAG assembled and binned from ERR7745410.
16S rRNAs recovered
1
16S recovered
TRUE
16S recovery software
barrnap;0.9;--kingdom bac
23S rRNAs recovered
1
5S rRNAs recovered
1
CheckM strain heterogeneity
100
ENA first public
2022-04-01
ENA last update
2022-04-01
External Id
SAMEA13520345
GTDB r202 classification
d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__RUG410;s__
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-04-01T08:27:46Z
INSDC last update
2022-04-01T08:27:46Z
INSDC status
public
MAG coverage depth
10.66
MAG coverage software
Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) 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-I-L_M_7_2493.83
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
binning parameters
Reads from ERR7745410 were assembled into contigs (ERZ4559957). The following read sets from this study were the most similar to ERR7745410 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745410,ERR7745402,ERR7745867,ERR7738274,ERR7745719,ERR7745819,ERR7738207,ERR7738165,ERR7738604,ERR7745427. 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 ERZ4559957. 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
2014-08-16
completeness approach
CheckM marker lineage: k__Bacteria (UID2565)
completeness score
90.7
completeness software
CheckM;1.1.2;lineage_wf
contamination score
1.14
contamination screening input
reads
contamination screening parameters
All reads in ERR7745410 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
ERR7745427_bin.87
intra-study species representative
ERR7745427_bin.87
investigation type
metagenome-assembled genome
isolation source
human feces
metagenomic source
human gut metagenome
most complete 16S rRNA recovered
0.9778212654924984
most complete 23S rRNA recovered
0.9401238816242258
most complete 5S rRNA recovered
0.9327731092436975
nucleic acid extraction
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
number of standard tRNAs extracted
38
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
ERS2586267
sample name
REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_M_7_2493.83
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
19