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SCGC AH-181-O17

Identifiers
BioSample: SAMN15485215; Sample name: AH-181-O17; SRA: SRS6975256
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_count354181
trimmerTrimmomatic v0.32
trim_parameters-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count343924
complexity_filter_threshold0
complexity_filtered_read_count343454
normalizerkmernorm 1.05
normalization_parameters-k 21 -t 30 -c 3
normalized_read_count84376
contamination_referenceGRCh38_AG665_mm10.fa
contamination_identity_threshold95
passed_contamination_filter84375
assemblerSPAdes genome assembler v3.9.0
assembly_parameters--careful --sc --phred-offset 33
passing_contig_length2200
all_contigs_count180
length_passing_contigs_count36
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_count36
final_contigs_assembled_length415259
max_contig_length40729
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:
SAMN15485215
ID:
15485215

BioProject SRA

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