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SCGC AH-173-B04

Identifiers
BioSample: SAMN09658087; Sample name: AH-173-B04; SRA: SRS3550734
Organism
Prevotella sp. AH-173-B04
cellular organisms; Bacteria; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella; unclassified Prevotella
Package
Microbe; version 1.0
Attributes
collection date2017-06-01
isolateAH-173-B04
broad-scale environmental contextdigestive tract
local-scale environmental contextfecal environment
environmental mediumfeces
geographic locationUSA
hostMus musculus
latitude and longitude37.77 N 122.39 W
elevation4 m
host body habitathindgut
host body productstool
host genotypeC57BL/6N
host sexmale
host subject idAH-173
host taxonomy ID10090 (10090)
isolatenot collected
strainnot collected
sample typesingle cell
analysis_project_typesingle amplified genome (SAG)
raw_read_count1184339
trimmerTrimmomatic v0.32
trim_parameters-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count1163308
complexity_filter_threshold0.05
complexity_filtered_read_count1162389
normalizerkmernorm 1.05
normalization_parameters-k 21 -t 30 -c 3
normalized_read_count298106
contamination_referenceGRCh38_AG665_mm10.fa
contamination_identity_threshold95
passed_contamination_filter298097
assemblerSPAdes genome assembler v3.9.0
assembly_parameters--careful --sc --phred-offset 33
passing_contig_length2200
all_contigs_count1069
length_passing_contigs_count105
contamination_databasesnt;AG-665_masked.fasta;Simons_negatives_170807.fasta;171127_simons_neg_curated.fasta
contaminated_contigs0
contamination_termshomo sapiens,human dna sequence,mus musculus,Delftia acidovorans,Achromobacter xylosoxidans,Stenotrophomonas maltophilia,Bradyrhizobium,AG-665_NODE_,AG-SIM-NEG_
contamination_alignment_length100
final_contigs_count105
final_contigs_assembled_length1124803
max_contig_length45103
gc_content47.8487344
completeness35.9
unique_marker_genes11
number_multi_copy0
checkM_classificationk__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;unresolved
SSU_classification_1no SSU regions found
SSU_contig_1NA
GTDBTk_lineaged__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:
SAMN09658087
ID:
9658087

BioProject SRA

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