bacterium
bcl2fastq_version
bcl2fastq 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_count
243939
trimmer
Trimmomatic v0.32
trim_parameters
-phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
trimmed_read_count
237798
complexity_filter_threshold
0
complexity_filtered_read_count
237577
normalizer
kmernorm 1.05
normalization_parameters
-k 21 -t 30 -c 3
normalized_read_count
39736
contamination_reference
GRCh38_AG665_mm10.fa
contamination_identity_threshold
95
passed_contamination_filter
39736
assembler
SPAdes genome assembler v3.9.0
assembly_parameters
--careful --sc --phred-offset 33
passing_contig_length
2200
all_contigs_count
160
length_passing_contigs_count
35
contamination_databases
nt;AG-665_masked.fasta;Simons_negatives_170807.fasta;171127_simons_neg_curated.fasta
contaminated_contigs
0
contamination_terms
homo sapiens,human dna sequence,mus musculus,Delftia acidovorans,Achromobacter xylosoxidans,Stenotrophomonas maltophilia,Bradyrhizobium,AG-665_NODE_,AG-SIM-NEG_
contamination_alignment_length
100
final_contigs_count
35
final_contigs_assembled_length
201360
max_contig_length
13672
gc_content
52
completeness
0
unique_marker_genes
0
number_multi_copy
0
checkM_classification
NA;unresolved
SSU_classification_1
no SSU regions found
SSU_contig_1
NA
host_id
AH-181
genotype
C57BL/6N
collection_date
2018-08-01
env_broad_scale
digestive tract
env_local_scale
fecal environment
env_medium
feces
geo_loc_name
USA: San Francisco
host
Mus musculus
lat_lon
37.77 N 122.39 W
elev
4 m
host_body_habitat
hindgut
host_body_product
stool
host_genotype
C57BL/6N
host_taxid
10090
analysis_project_type
single amplified genome (SAG)
isolate
not collected
strain
not collected
sample_type
single cell
isolation_source
fecal pellet
BioSampleModel
MISAG.host-associated