ERR7738209_bin.119_149_154_merged
uncultured Sordaria
This sample represents an uncultured Sordaria MAG assembled and binned from ERR7738209.
18S rRNAs recovered
22
18S recovered
TRUE
18S recovery software
barrnap;0.9;--kingdom euk
28S rRNAs recovered
26
5.8S rRNAs recovered
2
5S rRNAs recovered
100
BUSCO Completeness
92.3
BUSCO lineage
sordariomycetes_odb10
BUSCO string
C:92.3%[S:92.1%,D:0.2%],F:0.9%,M:6.8%,n:3817
ENA first public
2022-04-01
ENA last update
2022-04-01
External Id
SAMEA13794538
INSDC center alias
Stanford University School of Medicine
INSDC center name
stanford university school of medicine
INSDC first public
2022-04-01T08:28:16Z
INSDC last update
2022-04-01T08:28:16Z
INSDC status
public
MAG coverage depth
13.28
MAG coverage software
Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) 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
METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_B_2_2152.merged
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 ERR7738209 were assembled into contigs (ERZ4560053). The following read sets from this study were the most similar to ERR7738209 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738209,ERR7738161,ERR7738232,ERR7737972,ERR7737622,ERR7746144,ERR7738603,ERR7738651,ERR7738242,ERR7738599. 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 ERZ4560053. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning.
binning software
MetaBAT2 v2.15
collection date
2014-07-25
completeness approach
EukCC v2.1.0 based on similarity to taxid: 5148
completeness score
95.86
completeness software
EukCC v2.1.0; BUSCO v5.2.2
contamination score
0.38
contamination screening input
reads
contamination screening parameters
All reads in ERR7738209 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
investigation type
metagenome-assembled genome
isolation source
human feces
metagenomic source
human gut metagenome
most complete 18S rRNA recovered
0.9519178822258239
most complete 28S rRNA recovered
0.8243496916063288
most complete 5.8S rRNA recovered
0.525974025974026
most complete 5S rRNA recovered
1
nucleic acid extraction
https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
number of standard tRNAs extracted
415
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
ERS2586138
sample name
METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_B_2_2152.merged
sequencing method
Illumina NovaSeq 6000
tRNA extraction software
tRNAscan-SE;2.0.9;-E
tRep classification
Eukaryota|Ascomycota|Sordariomycetes|Sordariales|Sordariaceae|Sordaria|Sordaria macrospora
tRep species confidence
64.74140240672294
taxonomic classification
taxRep v0.5.3 vs UniRef100 (5 Mar 2020)
taxonomic identity marker
multi-marker approach
unique standard tRNAs extracted
20