SAMN09658469
External Id
d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Betaproteobacteriales;f__Burkholderiaceae;g__Parasutterella
GTDBTk_lineage
Gladstone Institutes
INSDC center name
2019-08-01T00:00:00Z
INSDC first public
2024-06-18T09:52:57.724Z
INSDC last update
SRS3550860
INSDC secondary accession
live
INSDC status
Microbe, viral or environmental
NCBI submission model
Microbe.1.0
NCBI submission package
SRS3550860
SRA accession
k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Parasutterella;s__?
SSU_classification_1
AH-177-M04_NODE_85 (1505 bp)
SSU_contig_1
428
all_contigs_count
single amplified genome (SAG)
analysis_project_type
SPAdes genome assembler v3.9.0
assembler
--careful --sc --phred-offset 33
assembly_parameters
k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Sutterellaceae;g__Sutterella;unresolved
checkM_classification
2017-06-01
collection date
53.45
completeness
0.05
complexity_filter_threshold
2877531
complexity_filtered_read_count
1
contaminated_contigs
100
contamination_alignment_length
nt;AG-665_masked.fasta;Simons_negatives_170807.fasta;171127_simons_neg_curated.fasta
contamination_databases
95
contamination_identity_threshold
GRCh38_AG665_mm10.fa
contamination_reference
homo sapiens,human dna sequence,mus musculus,Delftia acidovorans,Achromobacter xylosoxidans,Stenotrophomonas maltophilia,Bradyrhizobium,AG-665_NODE_,AG-SIM-NEG_
contamination_terms
4 m
elev
digestive tract
env biome
fecal environment
env feature
feces
http://purl.obolibrary.org/obo/NCIT_C13234
env_material
1705519
final_contigs_assembled_length
114
final_contigs_count
49.0351031
gc_content
USA
geo loc name
Mus musculus
http://purl.obolibrary.org/obo/NCBITaxon_10090
host
hindgut
http://purl.obolibrary.org/obo/UBERON_0001046
host body habitat
stool
http://www.ebi.ac.uk/efo/EFO_0007874
host body product
male
http://purl.obolibrary.org/obo/PATO_0000384
host sex
AH-177
host subject id
10090
host taxid
CD4-dnTGFBRII
host_genotype
AH-177-M04
isolate
37.77 N 122.39 W
lat lon
115
length_passing_contigs_count
95801
max_contig_length
-k 21 -t 30 -c 3
normalization_parameters
360758
normalized_read_count
kmernorm 1.05
normalizer
0
number_multi_copy
Sutterella sp. AH-177-M04
http://purl.obolibrary.org/obo/NCBITaxon_2269354
organism
359460
passed_contamination_filter
2200
passing_contig_length
2941806
raw_read_count
single cell
http://www.ebi.ac.uk/efo/EFO_0009899
sample type
SCGC AH-177-M04
title
-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trim_parameters
2882571
trimmed_read_count
Trimmomatic v0.32
trimmer
7
unique_marker_genes