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SCGC AH-177-G07

Identifiers
BioSample: SAMN09658412; Sample name: AH-177-G07; SRA: SRS3550778
Organism
Desulfonispora thiosulfatigenes
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Peptococcaceae; Desulfonispora
Package
Microbe; version 1.0
Attributes
collection date2017-06-01
broad-scale environmental contextdigestive tract
local-scale environmental contextfecal environment
environmental mediumfeces
geographic locationUSA
hostMus musculus
latitude and longitude
elevation4 m
host body habitathindgut
host body productstool
host genotypeCD4-dnTGFBRII
host sexmale
host subject idAH-177
host taxonomy ID10090 (Mus musculus)
isolatenot collected
strainnot collected
sample typesingle cell
analysis_project_typesingle amplified genome (SAG)
raw_read_count3297971
trimmerTrimmomatic v0.32
trim_parameters-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count3236437
complexity_filter_threshold0.05
complexity_filtered_read_count3230604
normalizerkmernorm 1.05
normalization_parameters-k 21 -t 30 -c 3
normalized_read_count308038
contamination_referenceGRCh38_AG665_mm10.fa
contamination_identity_threshold95
passed_contamination_filter305358
assemblerSPAdes genome assembler v3.9.0
assembly_parameters--careful --sc --phred-offset 33
passing_contig_length2200
all_contigs_count486
length_passing_contigs_count140
contamination_databasesnt;AG-665_masked.fasta;Simons_negatives_170807.fasta;171127_simons_neg_curated.fasta
contaminated_contigs1
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_count139
final_contigs_assembled_length1385955
max_contig_length52254
gc_content47.58293018
completeness41.35
unique_marker_genes24
number_multi_copy0
checkM_classificationk__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales_2;f__Peptococcaceae;o__Clostridiales;g__Desulfonispora;s__Desulfonispora_thiosulfatigenes
SSU_classification_1no SSU regions found
SSU_contig_1NA
GTDBTk_lineaged__Bacteria;p__Firmicutes;c__Desulfitobacteriia;o__Heliobacteriales
BioProject
PRJNA481120
Retrieve all samples from this project

Submission
Gladstone Institutes, Svetlana Lyalina; 2018-07-14
Accession:
SAMN09658412
ID:
9658412

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