barrnap (version 0.9)
16S recovery software
Yes
16s recovered
yes
23s recovered
yes
5s recovered
2024-03-27
ENA first public
ERC000047
ENA-CHECKLIST
40.5
%
GC content
CAU
INSDC center name
public
INSDC status
Bowtie (version 2.2.5) with jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1)
MAG coverage software
ERS18592526
SRA accession
ena-SAMPLE-TAB-22-03-2024-10:43:23:838-115489
Submitter Id
Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly quality
metaSPAdes hybrid (SPAdes version 3.13.1)
assembly software
coverage depth and k-mer binning. Scaffolds were filtered for min. length 1000bp and min. coverage 7.7815. Quality-controlled metagenomic reads were mapped back to the filtered scaffolds with Bowtie (version 2.2.5); the insert size was 0–1000 bp in very sensitive, non-deterministic, “fr” stranded mode with end-to-end alignment. Non-unique mappings and unaligned reads were discarded. The scaffold coverage depth was determined with the jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1). Scaffolds were broken into 10 kbp chunks for CONCOCT.
binning parameters
MetaBAT (version 2.12.1), CONCOCT (version 1.1.0), MaxBin (version 2.2.4), DASTool (version 1.1.2)
binning software
host associated gut microbiome
broad-scale environmental context
2017-02-14
collection date
98.7
%
completeness score
CheckM (version 1.1.2)
completeness software
0.7
%
contamination score
MAG_BA_Wujia_01: Metagenomic assembled genome (MAG) from colon contents of n=52, untreated, wild-type, male C57BL/6J/Ukj mice, aged 2-30 months. Full cohort assembly of all metagenomic samples assembled together from short and long read sequencing with metaSpades hybrid. Coverage and k-mer binning with MetaBAT (version 2.12.1), CONCOCT (version 1.1.0), and MaxBin (version 2.2.4) produced 252 bins which were refined into 181, high to medium quality MAGs via DASTool.
description
host associated gut microbiome
environmental medium
Germany
geographic location (country and/or sea)
50.9
DD
geographic location (latitude)
11.6
DD
geographic location (longitude)
mouse colon contents
isolation_source
host associated gut microbiome
local environmental context
mouse gut metagenome
metagenomic source
21
number of standard tRNAs extracted
uncultured Lachnospiraceae bacterium
organism
Baseline aging (BA); Aging-associated loss of metabolic host-microbiome-interactions in mice
project name
ERS18444878,ERS18444879,ERS18444880,ERS18444881,ERS18444882,ERS18444883,ERS18444884,ERS18444885,ERS18444886,ERS18444887,ERS18444888,ERS18444889,ERS18444890,ERS18444891,ERS18444892,ERS18444893,ERS18444894,ERS18444895,ERS18444896,ERS18444897,ERS18444898,ERS18444899,ERS18444900,ERS18444901,ERS18444902,ERS18444903,ERS18444904,ERS18444905,ERS18444906,ERS18444907,ERS18444908,ERS18444909,ERS18444910,ERS18444911,ERS18444912,ERS18444913,ERS18444914,ERS18444915,ERS18444916,ERS18444917,ERS18444918,ERS18444919,ERS18444920,ERS18444921,ERS18444922,ERS18444923,ERS18444924,ERS18444925,ERS18444926,ERS18444927,ERS18444928,ERS18444929,ERS18590020,ERS18590021,ERS18590022,ERS18590023,ERS18590024,ERS18590025,ERS18590026,ERS18590027
sample derived from
uncultured Lachnospiraceae bacterium
scientific_name
tRNAscan-SE (version 2.0.9)
tRNA extraction software
GTDB-Tk, r214
taxonomic classification
multi-marker approach
taxonomic identity marker
BA_Wujia_01
title