U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SCGC AH-181-P19

Identifiers
BioSample: SAMN15485230; Sample name: AH-181-P19; SRA: SRS6975272
Organism
bacterium
cellular organisms; Bacteria; unclassified Bacteria
Package
MISAG: single amplified genome, host-associated; version 6.0
Attributes
host taxonomy IDAH-181 (AH-181)
genotypeC57BL/6N
collection date2018-08-01
broad-scale environmental contextdigestive tract
local-scale environmental contextfecal environment
environmental mediumfeces
geographic locationUSA: San Francisco
hostMus musculus
latitude and longitude37.77 N 122.39 W
elevation4 m
host body habitathindgut
host body productstool
host genotypeC57BL/6N
host taxonomy ID10090 (10090)
isolatenot collected
strainnot collected
sample typesingle cell
isolation sourcefecal pellet
bcl2fastq_versionbcl2fastq v2.17.1.14
bcl2fastq_parameters--sample-sheet /mnt/scgc_raw/data/nextseq/181005_NB501011_0062_AH7YLNAFXY/SampleSheet.csv.2018-10-06-1505-01.rc.csv --loading-threads 12 --demultiplexing-threads 12 --processing-threads 40 --writing-threads 12 --barcode-mismatches 0 --no-lane-splitting --runfolder-dir /mnt/scgc_raw/data/nextseq/181005_NB501011_0062_AH7YLNAFXY
raw_read_count263384
trimmerTrimmomatic v0.32
trim_parameters-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count255169
complexity_filter_threshold0
complexity_filtered_read_count254015
normalizerkmernorm 1.05
normalization_parameters-k 21 -t 30 -c 3
normalized_read_count77605
contamination_referenceGRCh38_AG665_mm10.fa
contamination_identity_threshold95
passed_contamination_filter77605
assemblerSPAdes genome assembler v3.9.0
assembly_parameters--careful --sc --phred-offset 33
passing_contig_length2200
all_contigs_count304
length_passing_contigs_count62
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_count62
final_contigs_assembled_length444281
max_contig_length44113
gc_content54
completeness0
unique_marker_genes0
number_multi_copy0
checkM_classificationNA;unresolved
SSU_classification_1no SSUs were classified
SSU_contig_1NA
analysis_project_typesingle amplified genome (SAG)
Description

Keywords: GSC:MIxS;MISAG:6.0

BioProject
PRJNA481120
Retrieve all samples from this project

Submission
Gladstone Institutes, Svetlana Lyalina; 2020-07-08
Accession:
SAMN15485230
ID:
15485230

BioProject SRA

Supplemental Content

Related information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
You are here: NCBI > DNA & RNA > BioSample
Support Center