Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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don't find Strain heterogeneity info #371

Closed nashanghenzan closed 1 year ago

nashanghenzan commented 1 year ago

where are Strain heterogeneity infos of checkm output? i don't find it anywhere, my bin_stats_ext.tsv just shows: TSB_bin.1.strict {'GC std': 0.020564892167108596, '# genomes': 2258, 'Genome size': 3608043, 'Longest contig': 29061, 'GCN0': ['PF12169', 'TIGR00095', 'TIGR00409', 'PF00471', 'PF02075', 'PF01043', 'PF01351', 'PF00366', 'PF04560', 'PF02491', 'PF03719', 'PF07516', 'PF06071', 'TIGR00595', 'PF01624', 'PF00333', 'PF02224', 'TIGR00344', 'PF03948', 'PF00347', 'TIGR03598', 'PF00238', 'PF00861', 'PF07499', 'TIGR01063', 'PF02527', 'PF01121', 'PF11967', 'PF01330', 'PF02912', 'TIGR00019', 'TIGR00460', 'PF01715', 'PF02565', 'TIGR00064', 'TIGR01499', 'TIGR01079', 'TIGR00442', 'PF00253', 'PF00281', 'PF00673', 'PF02367', 'PF13603', 'PF00410', 'TIGR00420', 'PF01783', 'TIGR01143', 'TIGR02393'], 'GCN1': ['PF01509', 'PF00298', 'PF00203', 'PF00035', 'PF01196', 'PF00411', 'PF02096', 'PF00189', 'PF01281', 'TIGR00392', 'PF00181', 'PF00312', 'TIGR00575', 'PF00177', 'PF01193', 'PF01765', 'PF01409', 'PF02130', 'TIGR01394', 'PF03947', 'TIGR01083', 'TIGR01085', 'PF01782', 'PF02410', 'PF04563', 'TIGR00362', 'TIGR03723', 'TIGR03725', 'TIGR01951', 'PF03485', 'PF04998', 'PF00276', 'PF04561', 'PF06421', 'TIGR00593', 'PF01250', 'PF02576', 'PF00318', 'PF02033', 'PF01018', 'TIGR00615', 'PF03147', 'PF04997', 'PF00380', 'PF01084', 'PF00334', 'PF12631', 'PF00252', 'TIGR00755', 'TIGR03594', 'PF04565', 'PF11987', 'PF02699', 'TIGR01750', 'PF05698', 'PF00828', 'TIGR00020', 'PF00164', 'PF07497', 'PF02768', 'TIGR00922', 'TIGR02075', 'PF01000', 'PF01119', 'PF00572', 'PF00750', 'PF01746', 'PF01195', 'PF00466', 'TIGR00329', 'PF00453', 'PF08459', 'PF05491', 'PF13932', 'PF01016', 'TIGR01302', 'PF01245', 'PF02091', 'TIGR03302', 'PF01795', 'PF00831', 'PF01386', 'PF06418', 'PF00297', 'TIGR02432', 'PF03652', 'PF03946', 'TIGR03263', 'PF00542', 'PF00712', 'PF01687', 'PF03726', 'PF01192', 'PF02873', 'PF00687', 'PF01649', 'TIGR00041', 'PF01416', 'TIGR00214', 'PF00623', 'TIGR00445', 'PF04977', 'PF04983', 'TIGR01059', 'PF00627', 'PF00830', 'PF02575', 'PF05190', 'PF05000', 'PF00886', 'TIGR00186', 'PF12344', 'PF08529', 'TIGR01133', 'TIGR00422', 'PF00344', 'PF14450', 'PF00163', 'PF00829', 'PF02403', 'PF00237', 'PF00684', 'TIGR01145', 'TIGR00436', 'TIGR00435', 'PF13184', 'PF10396', 'PF10385', 'PF05697', 'PF00584', 'PF02978', 'TIGR01087', 'PF00573', 'PF02092'], 'GCN2': ['PF00338', 'PF04760', 'PF00889', 'PF03484', 'PF00562', 'PF01668'], 'marker lineage': 'k__Bacteria', 'GC': 0.5651105508032912, 'GCN4': [], '# scaffolds': 845, 'Completeness': 73.84852801519467, 'GCN3': [], 'GCN5+': [], '# contigs': 909, 'Translation table': 11, '# markers': 188, 'Coding density': 0.8563772660137365, 'Mean contig length': 3967.3828382838283, '# marker sets': 117, 'N50 (contigs)': 5570, '1': 134, '0': 48, '3': 0, '2': 6, 'Longest scaffold': 29061, '4': 0, '5+': 0, 'Contamination': 1.6429249762583096, '# predicted genes': 3777, 'N50 (scaffolds)': 6002, '# ambiguous bases': 1692, 'Mean scaffold length': 4269.873372781065}