ERR7738620_bin.12
This sample represents an uncultured Coriobacteriales bacterium MAG assembled and binned from ERR7738620.
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
SAMEA13478023
GTDB r202 classification
d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01;s__QAMH01 sp900556425
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-04-01T08:27:11Z
INSDC last update
2022-04-01T08:27:11Z
INSDC status
public
MAG coverage depth
12.67
MAG coverage software
Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) 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_SUBJECT_CONTIGS_1500_ASSEMBLY_K77_MERGED__Pilot_MoBio_Fiber_C_24_1038.12
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 ERR7738620 were assembled into contigs (ERZ4558877). The following read sets from this study were the most similar to ERR7738620 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738620,ERR7738633. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 2 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4558877. Depth information for all 2 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
2017
completeness approach
CheckM marker lineage: p__Actinobacteria (UID2112)
completeness score
100
completeness software
CheckM;1.1.2;lineage_wf
contamination score
0.81
contamination screening input
reads
contamination screening parameters
All reads in ERR7738620 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)
USA
geographic location (elevation)
29
geographic location (latitude)
37.4275
geographic location (longitude)
-122.1697
inter-study species representative
ERR7738620_bin.12
intra-study species representative
ERR7738620_bin.12
investigation type
metagenome-assembled genome
isolation source
human feces
metagenomic source
human gut metagenome
most complete 16S rRNA recovered
0.9817351598173516
most complete 23S rRNA recovered
0.7002752924982795
most complete 5S rRNA recovered
0.907563025210084
nucleic acid extraction
https://doi.org/10.1016/j.cell.2021.06.019
number of standard tRNAs extracted
45
project name
Metagenome sequencing of Californian gut microbiome
reassembly post binning
No
reference for biomaterial
https://doi.org/10.1016/j.cell.2021.06.019
sample collection device or method
https://doi.org/10.1016/j.cell.2021.06.019
sample derived from
SRS9383817
sample name
REFINED_METABAT215_SUBJECT_CONTIGS_1500_ASSEMBLY_K77_MERGED__Pilot_MoBio_Fiber_C_24_1038.12
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
20