ERR7738221_bin.35
uncultured Clostridia bacterium
This sample represents an uncultured Clostridia bacterium MAG assembled and binned from ERR7738221.
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
0
ENA first public
2022-04-01
ENA last update
2022-04-01
External Id
SAMEA13525069
GTDB r202 classification
d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1242;g__UBA6345;s__
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-04-01T08:27:37Z
INSDC last update
2022-04-01T08:27:37Z
INSDC status
public
MAG coverage depth
60.33
MAG coverage software
Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) 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_N_19_1307.35
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 ERR7738221 were assembled into contigs (ERZ4561408). The following read sets from this study were the most similar to ERR7738221 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738221,ERR7738256,ERR7738629,ERR7738574,ERR7738605,ERR7738206,ERR7746012,ERR7738267,ERR7738233,ERR7738212. 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 ERZ4561408. 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
2013-10-27
completeness approach
CheckM marker lineage: k__Bacteria (UID2329)
completeness score
52.94
completeness software
CheckM;1.1.2;lineage_wf
contamination score
0.56
contamination screening input
reads
contamination screening parameters
All reads in ERR7738221 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
ERR7738630_bin.173
intra-study species representative
ERR7738608_bin.207
investigation type
metagenome-assembled genome
isolation source
human feces
metagenomic source
human gut metagenome
most complete 16S rRNA recovered
0.32354859752120024
most complete 23S rRNA recovered
0.5763936682725396
most complete 5S rRNA recovered
0.957983193277311
nucleic acid extraction
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
number of standard tRNAs extracted
22
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
ERS2585722
sample name
REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_N_19_1307.35
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
14