| collection date | 2013-09-07 |
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| broad-scale environmental context | terrestrial biome |
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| local-scale environmental context | human-associated habitat |
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| environmental medium | feces |
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| geographic location | Tanzania |
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| investigation type | metagenome-assembled genome |
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| isolation source | human feces |
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| project name | Metagenome sequencing of Hadza gut microbiome |
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| reference for biomaterial | https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 |
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| sample collection device or method | https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 |
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| sample name | REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112.310 |
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| 16S rRNAs recovered | 0 |
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| 16S recovered | FALSE |
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| 16S recovery software | barrnap;0.9;--kingdom arc |
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| 23S rRNAs recovered | 0 |
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| 5S rRNAs recovered | 0 |
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| CheckM strain heterogeneity | 0 |
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| ENA first public | 2022-04-01 |
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| ENA last update | 2022-04-01 |
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| ENA-CHECKLIST | ERC000011 |
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| External Id | SAMEA13475686 |
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| GTDB r202 classification | d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera;s__Methanosphaera stadtmanae |
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| INSDC center alias | Stanford University School of Medicine |
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| INSDC center name | stanford university school of medicine |
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| INSDC first public | 2022-04-01T08:24:49Z |
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| INSDC last update | 2022-04-01T08:24:49Z |
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| INSDC status | public |
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| MAG coverage depth | 19.27 |
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| MAG coverage software | Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. |
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| Submitter Id | REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112.310 |
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| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics. |
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| assembly software | metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz |
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| binning parameters | Reads from ERR7746411 were assembled into contigs (ERZ4568013). The following read sets from this study were the most similar to ERR7746411 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746411,ERR7745759,ERR7745743,ERR7747255,ERR7738557,ERR7745408,ERR7738626,ERR7747394,ERR7745823,ERR7746349. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4568013. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin. |
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| binning software | MetaBAT2 v2.15; MAGpurify v2.1.0 |
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| completeness approach | CheckM marker lineage: p__Euryarchaeota (UID3) |
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| completeness score | 97.6 |
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| completeness software | CheckM;1.1.2;lineage_wf |
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| contamination score | 0 |
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| contamination screening input | reads |
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| contamination screening parameters | All reads in ERR7746411 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2). |
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| geographic location (elevation) | 1287 |
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| geographic location (latitude) | -3.55 |
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| geographic location (longitude) | -34.58 |
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| inter-study species representative | GUT_GENOME143494 |
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| intra-study species representative | ERR7738600_bin.106 |
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| metagenomic source | human gut metagenome |
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| nucleic acid extraction | https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 |
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| number of standard tRNAs extracted | 39 |
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| reassembly post binning | No |
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| sample derived from | ERS2585536 |
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| sequencing method | Illumina NovaSeq 6000 |
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| tRNA extraction software | tRNAscan-SE;2.0.9;-A |
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| taxonomic classification | GTDB-TK v1.7.0, r202 database, default parameters |
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| taxonomic identity marker | multi-marker approach |
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| unique standard tRNAs extracted | 20 |
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