| collection date | 2017-06-01 |
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| isolate | AH-177-P20 |
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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 |
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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 | CD4-dnTGFBRII |
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| host sex | male |
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| host subject id | AH-177 |
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| host taxonomy ID | 10090 (10090) |
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| sample type | single cell |
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| analysis_project_type | single amplified genome (SAG) |
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| raw_read_count | 2762192 |
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| trimmer | Trimmomatic v0.32 |
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| trim_parameters | -phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36 |
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| trimmed_read_count | 2687704 |
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| complexity_filter_threshold | 0.05 |
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| complexity_filtered_read_count | 2683767 |
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| normalizer | kmernorm 1.05 |
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| normalization_parameters | -k 21 -t 30 -c 3 |
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| normalized_read_count | 125109 |
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| contamination_reference | GRCh38_AG665_mm10.fa |
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| contamination_identity_threshold | 95 |
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| passed_contamination_filter | 125107 |
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| assembler | SPAdes genome assembler v3.9.0 |
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| assembly_parameters | --careful --sc --phred-offset 33 |
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| passing_contig_length | 2200 |
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| all_contigs_count | 241 |
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| length_passing_contigs_count | 75 |
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| contamination_databases | nt;AG-665_masked.fasta;Simons_negatives_170807.fasta;171127_simons_neg_curated.fasta |
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| contaminated_contigs | 0 |
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| contamination_terms | homo sapiens,human dna sequence,mus musculus,Delftia acidovorans,Achromobacter xylosoxidans,Stenotrophomonas maltophilia,Bradyrhizobium,AG-665_NODE_,AG-SIM-NEG_ |
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| contamination_alignment_length | 100 |
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| final_contigs_count | 75 |
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| final_contigs_assembled_length | 547159 |
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| max_contig_length | 23190 |
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| gc_content | 56.40079026 |
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| completeness | 31.23 |
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| unique_marker_genes | 11 |
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| number_multi_copy | 0 |
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| checkM_classification | k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;unresolved |
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| SSU_classification_1 | k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__? |
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| SSU_contig_1 | AH-177-P20_NODE_15 (1489 bp) |
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| GTDBTk_lineage | d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes |
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