16S recovered
Yes
16S recovery software
barrnap:0.9
ENA first public
2022-02-22
ENA last update
2022-02-22
External Id
SAMEA13058561
INSDC center alias
ETH ZURICH
INSDC center name
ETH ZURICH
INSDC first public
2022-02-22T16:51:25Z
INSDC last update
2022-02-22T16:51:25Z
INSDC status
public
Submitter Id
E.malaspinii_MAG_MP1648_PBLIHF
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
flye;2.9;defaults
collection date
2011-04-28
completeness approach
Average of checkm and anvi'o (marker-gene based) and contiguous chromosome-level assembly
completeness score
96.81
completeness software
checkm and anvi'o
contamination score
0
contamination screening input
contiguous chromosome-level assembly and phylogenetic inspection of duplicated marker genes
environment (biome)
Ocean Water
environment (feature)
Ocean water
environment (material)
Ocean water
feature prediction
prokka:1.4;Prodigal:002006;Aragorn:001002;barrnap:0.9;minced:0.4.2
geographic location (country and/or sea)
Pacific Ocean
geographic location (depth)
4018
geographic location (latitude)
-5.75
geographic location (longitude)
-170.7407
investigation type
metagenome
isolation source
ocean water
metagenomic source
marine metagenome
nucleic acid amplification
PacBio kits SMRTbell gDNA Sample amplification kit (100-980-000)
number of standard tRNAs extracted
21
project name
Biosynthetic potential of the global ocean microbiome
reassembly post binning
No
reference for biomaterial
https://doi.org/10.1038/s42003-021-02112-2
relevant standard operating procedures
PacBio HiFi reads were quality controlled (pbclip) and mapped against a short-read metagenome assembled genome of the species to select for reads mapping with an identity >=99% over >=2kbp. The selected reads were assembled with Flye.
sample derived from
SAMN05421555
sample name
E.malaspinii_MAG_MP1648_PBLIHF
sequencing method
PacBio HiFi
size fraction selected
0.8-20 micrometers
tRNA extraction software
Aragorn:001002
taxonomic classification
GTDBTk:v1.5.0, Database:r202, d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__;g__;s__
taxonomic identity marker
multi-gene approach (GTDBTk:v1.5.0)