| host taxonomy ID | AH-181 (AH-181) |
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| genotype | C57BL/6N |
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| collection date | 2018-08-01 |
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| broad-scale environmental context | digestive tract |
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| local-scale environmental context | fecal environment |
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| environmental medium | feces |
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| geographic location | USA: San Francisco |
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| host | Mus musculus |
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| latitude and longitude | 37.77 N 122.39 W |
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| elevation | 4 m |
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| host body habitat | hindgut |
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| host body product | stool |
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| host genotype | C57BL/6N |
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| host taxonomy ID | 10090 (10090) |
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| isolate | not collected |
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| strain | not collected |
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| sample type | single cell |
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| isolation source | fecal pellet |
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| 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 | 329506 |
|---|
| trimmer | Trimmomatic v0.32 |
|---|
| trim_parameters | -phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36 |
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| trimmed_read_count | 322245 |
|---|
| complexity_filter_threshold | 0 |
|---|
| complexity_filtered_read_count | 321801 |
|---|
| normalizer | kmernorm 1.05 |
|---|
| normalization_parameters | -k 21 -t 30 -c 3 |
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| normalized_read_count | 96463 |
|---|
| contamination_reference | GRCh38_AG665_mm10.fa |
|---|
| contamination_identity_threshold | 95 |
|---|
| passed_contamination_filter | 96463 |
|---|
| assembler | SPAdes genome assembler v3.9.0 |
|---|
| assembly_parameters | --careful --sc --phred-offset 33 |
|---|
| passing_contig_length | 2200 |
|---|
| all_contigs_count | 499 |
|---|
| length_passing_contigs_count | 66 |
|---|
| 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 | 66 |
|---|
| final_contigs_assembled_length | 704876 |
|---|
| max_contig_length | 72734 |
|---|
| gc_content | 46 |
|---|
| completeness | 4 |
|---|
| unique_marker_genes | 1 |
|---|
| number_multi_copy | 0 |
|---|
| checkM_classification | k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Neorickettsia;s__Neorickettsia_risticii |
|---|
| SSU_classification_1 | k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospiraceae_NK4A136_group;s__? |
|---|
| SSU_contig_1 | AH-181-K18_NODE_3 (1494 bp) |
|---|
| analysis_project_type | single amplified genome (SAG) |
|---|