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"ANON10_Brennan2019_SRR7289008_4136", "ANON9_Brennan2019_SRR7289008_524", "ANON8_Brennan2019_SRR7289008_237", "ANON7_Brennan2019_SRR7289008_234", "ANON6_Brennan2019_SRR7289008_356", "ANON5_Brennan2019_SRR7289008_105", "ANON4_Brennan2019_SRR7289008_29", "ANON3_Brennan2019_SRR7288995_2985", "ANON2_Brennan2019_SRR7288995_499", "ANON1_Brennan2019_SRR7288995_5" ], "fragment_selection": "Best HSP per query/subject. Highest-bit-score fragment per reference across queries. Subject orientation follows its BLAST query; MAFFT adjusts direction.", "input_sha256": "bffce76ae608242a6725ebbc11b0a7610aafd8616694a2ba0cbfa666645816ec", "program_sha256": { "085_NJBS_rbcl.R": "5dd4e6a99a8bff81d3b9dc003fe05b537dc970651de791fe37627ceb75c15778", "115_treePlot_pSCOPE.R": "14d5067501e27bfc5702f240d9c6fb04f29d827a60ad131ccf42dd6247fbb1b3", "phyloBARCODER_rbcl.py": "9f257fd5a8621e4e9bf26a54c85bb7c698ecb1e6edaeabc7a8623e92618dd69c" }, "reference_provenance": { "source": "https://figshare.com/articles/dataset/rbcL_all_Jan2016_full_headers_fasta/3827622", "doi": "10.6084/m9.figshare.3827622.v1", "license": { "value": 1, "name": "CC BY 4.0", "url": "https://creativecommons.org/licenses/by/4.0/" }, "records": 87270, "organism_labels": 38008, "excluded": [ { "header": "530354756 JX944788 Liquidambar_formosana", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "951312466 KT779528 Capsicum_annuum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": 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"reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534265 KC479099 Leucopogon_denticulatus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534267 KC479100 Coleanthera_myrtoides", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534269 KC479101 Astroloma_microdonta", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534271 KC479102 Leucopogon_sp._Murdoch", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534273 KC479103 Conostephium_pendulum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534275 KC479104 Leucopogon_sp._Coomallo", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534277 KC479105 Leucopogon_propinquus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534279 KC479106 Astroloma_pedicellatum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534281 KC479107 Astroloma_acervatum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534283 KC479108 Leucopogon_woodsii", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534285 KC479109 Leucopogon_opponens", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534287 KC479110 Leucopogon_planifolius", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534289 KC479111 Astroloma_glaucescens", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534291 KC479112 Astroloma_serratifolium", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534293 KC479113 Conostephium_preissii", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534295 KC479114 Styphelia_melaleucoides_var._ovata", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534296 KC479115 Astroloma_chloranthum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534298 KC479116 Astroloma_baxteri", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534300 KC479117 Leucopogon_sp._Coujinup", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534302 KC479118 Leucopogon_sp._short_style", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534304 KC479119 Leucopogon_sp._Newdegate", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534306 KC479120 Leucopogon_sp._Northern_ciliate", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534308 KC479121 Conostephium_minus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534310 KC479122 Leucopogon_sp._Mid_West", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534312 KC479123 Leucopogon_elegans", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "551534314 KC479124 Astroloma_acervatum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "377648379 JF419563 Nicotiana_attenuata", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "407911679 JQ923431 Ipomoea_batatas", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "451172652 KC150874 Quercus_ilex", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "565824428 KF697233 Phragmites_australis", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "565824430 KF697234 Phragmites_australis", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "241696 S75127 Taxodium_distichum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076693 AF495762 Gongylocarpus_fruticulosus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076695 AF495763 Epilobium_rigidum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076697 AF495764 Xylonagra_arborea", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076699 AF495765 Gayophytum_heterozygum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076701 AF495766 Eremothera_boothii", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076703 AF495767 Oenothera_hartwegii", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076705 AF495768 Oenothera_glaucifolia", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076707 AF495769 Oenothera_anomala", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076709 AF495770 Oenothera_brachycarpa", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076711 AF495771 Oenothera_fruticosa", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076713 AF495772 Chylismia_arenaria", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "28076716 AF495774 Megacorax_gracielanus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "30749202 AF022951 Calycanthus_occidentalis", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "54401455 AY772669 Elymus_sibiricus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "167275 L10216 Circaea_alpina", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "167279 L10225 Clarkia_xantiana", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "125380585 EF208123 Cucumis_sativus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168174 L10220 Fuchsia_cyrtandroides", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168206 L10227 Hauya_elegans", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168311 L10219 Lopezia_riesenbachia", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168317 L10221 Ludwigia_peruviana", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168319 L10222 Ludwigia_peploides", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168334 L10218 Lythrum_hyssopifolia", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "169646 L10223 Punica_granatum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "476751 L24073 Oryza_sativa", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "170188 L10226 Trapa_natans", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "4176298 AF013246 Siparuna_brasiliensis", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "4176300 AF022950 Hennecartia_omphalandra", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "2897113 AF030238 Pseudomonotes_tropenbosii", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "3403235 AF071544 Spinacia_oleracea", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "3403237 AF071545 Spinacia_oleracea", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "32966579 AY328025 Triticum_aestivum", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "68500782 DQ017796 Hyobanche_glabrata", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "68500783 DQ017797 Hyobanche_sanguinea", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "68500784 DQ017798 Harveya_coccinea", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "68500786 DQ017799 Harveya_stenosiphon", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "68500788 DQ017800 Harveya_capensis", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "168136 L10217 Chamerion_angustifolium", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "414070 X75478 Picea_abies", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "50978418 AJ786659 Limonium_gibertii", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "86211240 DQ355129 Stevia_rebaudiana", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "1303670 D28865 Acorus_calamus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "1679573 D28866 Acorus_gramineus", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "6967046 AJ271897 Pinus_halepensis", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "893366 D28867 Gloriosa_superba", "reason": "invalid DNA or shorter than 100 bp" }, { "header": "2765294 Y13116 Physena_sp._Schatz_2350", "reason": "invalid DNA or shorter than 100 bp" } ], "original_sha256": "116745ae9c8cc50f0d5829b30d294eeaf43ace589320fc61d9188d8d6442f03d", "modifications": "Replaced GI-only first header token with accession.giGI. Retained source sequence strings (uppercased). Genus inferred from first organism-name token. Higher taxonomy unavailable; not inferred. Built BLAST index. Taxonomic lineage supplemented from Bell RDP FASTA and NCBI Taxonomy; details in taxonomy_enrichment.", "reference_date": "January 2016", "citation": "Bell KL, Loeffler VM, Brosi BJ (2017). doi:10.3732/apps.1600110", "taxonomy_enrichment": { "source": "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz", "sha256": "37015aa6653e803de102c928ad2efccf96ffb1ed3514e5db47732124edb1857d", "records": 87270, "groups": { "Gymnosperms": 3628, "Eudicots": 56602, "Monocots": 21184, "Magnoliids": 3170, "Angiosperms": 2265, "Chloranthales": 117, "Nymphaeales": 128, "Ceratophyllales": 15, "Austrobaileyales": 157, "Unclassified-plants": 1, "Amborellales": 3 }, "match_methods": { "Bell_GI_sequence_taxid": 87247, "scientific_name": 13, "synonym": 7, "genus_scientific_name": 3 }, "clade_taxids": { "Gymnosperms": 1437180, "Monocots": 4447, "Eudicots": 71240, "Magnoliids": 232347, "Amborellales": 261009, "Nymphaeales": 261007, "Austrobaileyales": 82956, "Chloranthales": 261008, "Ceratophyllales": 91811 }, "bell_source": "https://doi.org/10.6084/m9.figshare.3827631.v1", "bell_zip_sha256": "fc6c312be4efb00f4aeb0260549dd7b43f2134df4a9cbb6d04b7097495aad301", "policy": "Primary: Bell RDP FASTA joined by GI and verified sequence hash. Broad plant clade from supplied taxid (merged IDs resolved); named family retained from Bell lineage. Fallback: Exact scientific name, then accepted synonym; only Viridiplantae matches. Ambiguous conflicting group/family assignments are rejected. If species-name match unavailable, unique/concordant genus lineage is used and recorded. Original organism label retained. Family is nearest family-ranked ancestor. Unknown groups/families explicit." } } }