Daniel Lundin
commited on
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32a0fbc
1
Parent(s):
b7659e8
CheckM and GTDBtk data
Browse files
testdata/checkm.lineage_wf.qa_2.tsv
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Bin Id Marker lineage # genomes # markers # marker sets Completeness Contamination Strain heterogeneity Genome size (bp) # ambiguous bases # scaffolds # contigs N50 (scaffolds) N50 (contigs) Mean scaffold length (bp) Mean contig length (bp) Longest scaffold (bp) Longest contig (bp) GC GC std (scaffolds > 1kbp) Coding density Translation table # predicted genes 0 1 2 3 4 5+
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GCA_002688505.1_ASM268850v1_genomic k__Bacteria (UID2495) 2993 136 80 77.08 0.00 0.00 271175 2 1 1 271175 271173 271175 271173 271175 271173 15.4 0.00 89.63 4 257 20 116 0 0 0 0
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GCF_004296495.1_ASM429649v1_genomic k__Bacteria (UID2495) 2993 136 80 64.89 0.00 0.00 200316 0 1 1 200316 200316 200316 200316 200316 200316 15.3 0.00 93.12 11 198 33 103 0 0 0 0
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testdata/gtdbtk.ar122.summary.tsv
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user_genome classification fastani_reference fastani_reference_radius fastani_taxonomy fastani_ani fastani_af closest_placement_reference closest_placement_radius closest_placement_taxonomy closest_placement_ani closest_placement_af pplacer_taxonomy classification_method note other_related_references(genome_id,species_name,radius,ANI,AF) msa_percent translation_table red_value warnings
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testdata/gtdbtk.bac120.summary.tsv
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user_genome classification fastani_reference fastani_reference_radius fastani_taxonomy fastani_ani fastani_af closest_placement_reference closest_placement_radius closest_placement_taxonomy closest_placement_ani closest_placement_af pplacer_taxonomy classification_method note other_related_references(genome_id,species_name,radius,ANI,AF) msa_percent translation_table red_value warnings
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GCA_002688505.1_ASM268850v1_genomic d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Stammera;s__Stammera capleta GCA_002688505.1 95.0 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Stammera;s__Stammera capleta 100.0 0.99 GCA_002688505.1 95.0 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Stammera;s__Stammera capleta 100.0 0.99 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__;s__ taxonomic classification defined by topology and ANI topological placement and ANI have congruent species assignments N/A 64.13 4 N/A N/A
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GCF_004296495.1_ASM429649v1_genomic d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Nardonella;s__Nardonella dryophthoridicola GCF_004296495.1 95.0 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Nardonella;s__Nardonella dryophthoridicola 100.0 1.0 GCF_004296495.1 95.0 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Nardonella;s__Nardonella dryophthoridicola 100.0 1.0 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Nardonella;s__ taxonomic classification defined by topology and ANI topological placement and ANI have congruent species assignments GCF_004296515.1, s__Nardonella sp004296515, 95.0, 78.8, 0.58; GCF_004296535.1, s__Nardonella sp004296535, 95.0, 78.65, 0.58; GCF_004296475.1, s__Nardonella sp004296475, 95.0, 78.51, 0.61 49.08 11 N/A N/A
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