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SCGC AH-177-D07

Identifiers
BioSample: SAMN09658371; Sample name: AH-177-D07; SRA: SRS3550836
Organism
Clostridium sp. AH-177-D07
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Clostridiaceae; Clostridium; unclassified Clostridium
Package
Microbe; version 1.0
Attributes
collection date2017-06-01
isolateAH-177-D07
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 genotypeCD4-dnTGFBRII
host sexmale
host subject idAH-177
host taxonomy ID10090 (10090)
sample typesingle cell
analysis_project_typesingle amplified genome (SAG)
raw_read_count4533281
trimmerTrimmomatic v0.32
trim_parameters-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count4458763
complexity_filter_threshold0.05
complexity_filtered_read_count4449363
normalizerkmernorm 1.05
normalization_parameters-k 21 -t 30 -c 3
normalized_read_count615124
contamination_referenceGRCh38_AG665_mm10.fa
contamination_identity_threshold95
passed_contamination_filter615123
assemblerSPAdes genome assembler v3.9.0
assembly_parameters--careful --sc --phred-offset 33
passing_contig_length2200
all_contigs_count1412
length_passing_contigs_count310
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_count310
final_contigs_assembled_length3023303
max_contig_length118737
gc_content40.50454089
completeness19.78
unique_marker_genes9
number_multi_copy0
checkM_classificationk__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;f__Peptostreptococcaceae;g__Clostridium;s__
SSU_classification_1no SSUs were classified
SSU_contig_1NA
GTDBTk_lineaged__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J
BioProject
PRJNA481120
Retrieve all samples from this project

Submission
Gladstone Institutes, Svetlana Lyalina; 2018-07-14
Accession:
SAMN09658371
ID:
9658371

BioProject SRA

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