SCGC AH-177-D13

Identifiers: BioSample: SAMN09658374; Sample name: AH-177-D13; SRA: SRS3550826

Organism: Prevotella sp. AH-177-D13
cellular organisms; Bacteria; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella; unclassified Prevotella

Package: Microbe; version 1.0

Attributes

collection date	2017-06-01
isolate	AH-177-D13
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	CD4-dnTGFBRII
host sex	male
host subject id	AH-177
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	3506890
trimmer	Trimmomatic v0.32
trim_parameters	-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count	3446815
complexity_filter_threshold	0.05
complexity_filtered_read_count	3445093
normalizer	kmernorm 1.05
normalization_parameters	-k 21 -t 30 -c 3
normalized_read_count	183845
contamination_reference	GRCh38_AG665_mm10.fa
contamination_identity_threshold	95
passed_contamination_filter	183845
assembler	SPAdes genome assembler v3.9.0
assembly_parameters	--careful --sc --phred-offset 33
passing_contig_length	2200
all_contigs_count	248
length_passing_contigs_count	77
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	77
final_contigs_assembled_length	844197
max_contig_length	55981
gc_content	46.97434367
completeness	30.43
unique_marker_genes	14
number_multi_copy	0
checkM_classification	k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;unresolved
SSU_classification_1	no SSUs were classified
SSU_contig_1	NA
GTDBTk_lineage	d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella

BioProject: PRJNA481120
Retrieve all samples from this project

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

Accession:: SAMN09658374
ID:: 9658374

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