SCGC AH-173-B02

Identifiers: BioSample: SAMN09658085; Sample name: AH-173-B02; SRA: SRS3550739

Organism: Holdemanella biformis
cellular organisms; Bacteria; Bacillati; Bacillota; Erysipelotrichia; Erysipelotrichales; Erysipelotrichaceae; Holdemanella

Package: Microbe; version 1.0

Attributes

collection date	2017-06-01
broad-scale environmental context	digestive tract
local-scale environmental context	fecal environment
environmental medium	feces
geographic location	USA
host	Mus musculus
latitude and longitude	37.77 N 122.39 W
elevation	4 m
host body habitat	hindgut
host body product	stool
host genotype	C57BL/6N
host sex	male
host subject id	AH-173
host taxonomy ID	10090 (10090)
isolate	not collected
strain	not collected
sample type	single cell
analysis_project_type	single amplified genome (SAG)
raw_read_count	1346456
trimmer	Trimmomatic v0.32
trim_parameters	-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count	1320972
complexity_filter_threshold	0.05
complexity_filtered_read_count	1320064
normalizer	kmernorm 1.05
normalization_parameters	-k 21 -t 30 -c 3
normalized_read_count	233024
contamination_reference	GRCh38_AG665_mm10.fa
contamination_identity_threshold	95
passed_contamination_filter	233009
assembler	SPAdes genome assembler v3.9.0
assembly_parameters	--careful --sc --phred-offset 33
passing_contig_length	2200
all_contigs_count	915
length_passing_contigs_count	107
contamination_databases	nt;AG-665_masked.fasta;Simons_negatives_170807.fasta;171127_simons_neg_curated.fasta
contaminated_contigs	0
contamination_terms	homo sapiens,human dna sequence,mus musculus,Delftia acidovorans,Achromobacter xylosoxidans,Stenotrophomonas maltophilia,Bradyrhizobium,AG-665_NODE_,AG-SIM-NEG_
contamination_alignment_length	100
final_contigs_count	107
final_contigs_assembled_length	851769
max_contig_length	79305
gc_content	52.92009923
completeness	28.95
unique_marker_genes	2
number_multi_copy	0
checkM_classification	k__Bacteria;p__Tenericutes;c__Mollicutes;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Solobacterium;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__Eubacterium_biforme
SSU_classification_1	k__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum;s__?
SSU_contig_1	AH-173-B02_NODE_31 (1526 bp)
GTDBTk_lineage	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum

BioProject: PRJNA481120
Retrieve all samples from this project

Submission: Gladstone Institutes, Svetlana Lyalina; 2018-07-14

Accession:: SAMN09658085
ID:: 9658085

BioProject SRA

BioSample

National Center for Biotechnology Information

Result Filters

Send to:

SCGC AH-173-B02

Supplemental Content

Related information

Recent activity