SCGC AH-173-F08

Identifiers: BioSample: SAMN09658161; Sample name: AH-173-F08; SRA: SRS3550929

Organism: Lactobacillaceae bacterium AH-173-F08
cellular organisms; Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; unclassified Lactobacillaceae

Package: Microbe; version 1.0

Attributes

collection date	2017-06-01
isolate	AH-173-F08
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)
sample type	single cell
analysis_project_type	single amplified genome (SAG)
raw_read_count	342454
trimmer	Trimmomatic v0.32
trim_parameters	-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count	334922
complexity_filter_threshold	0.05
complexity_filtered_read_count	334670
normalizer	kmernorm 1.05
normalization_parameters	-k 21 -t 30 -c 3
normalized_read_count	70563
contamination_reference	GRCh38_AG665_mm10.fa
contamination_identity_threshold	95
passed_contamination_filter	70563
assembler	SPAdes genome assembler v3.9.0
assembly_parameters	--careful --sc --phred-offset 33
passing_contig_length	2200
all_contigs_count	161
length_passing_contigs_count	52
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	52
final_contigs_assembled_length	364780
max_contig_length	37140
gc_content	47.83485937
completeness	8.62
unique_marker_genes	1
number_multi_copy	0
checkM_classification	k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;unresolved
SSU_classification_1	no SSU regions found
SSU_contig_1	NA
GTDBTk_lineage	d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Homeothermaceae;g__Homeothermus

BioProject: PRJNA481120
Retrieve all samples from this project

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

Accession:: SAMN09658161
ID:: 9658161

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