Run of program pandagma pan, version 2023-01-28 Run started at: Tue Feb 13 12:45:13 PM CST 2024 Run ended at: Tue Feb 13 01:35:31 PM CST 2024 Sequence type: nucleotide Parameter value clust_iden 0.90 clust_cov 0.50 extra_iden 0.80 mcl_inflation 1.6 strict_synt 1 pctl_low 25 pctl_med 50 pctl_hi 75 consen_prefix Phaseolus.pan2 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method alignment preferred_annot G19833.gnm2.ann1 Output directory for this run: out_pandagma Statistic value == Initial clusters (containing only genes within synteny blocks) Cluster file 06_syn_pan.clust.tsv num_of_clusters 27093 largest_cluster 24 modal_clst_size 8 num_at_mode 16455 seqs_clustered 189742 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 28885 largest_cluster 71 modal_clst_size 8 num_at_mode 16493 seqs_clustered 196603 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 3 genes per OG (>= 9 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 28885 largest_cluster 74 modal_clst_size>=3 9 num_at_mode>=3 16255 seqs_clustered 222033 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 27506 171 15285 1584 1252.4 phaac.Frijol_Bayo.gnm1.ann1 Main: 27062 6 15285 1608 1232.1 phaac.W6_15578.gnm2.ann1 Main: 29381 96 16662 1626 1298.5 phaco.PHA8298.gnm1.ann1 Main: 32525 93 16293 1617 1250.0 phalu.G27455.gnm1.ann1 Main: 27008 72 16701 1629 1303.7 phavu.5-593.gnm1.ann1 Main: 27383 90 16290 1602 1260.2 phavu.G19833.gnm2.ann1 Main: 27152 90 16359 1623 1296.8 phavu.LaborOvalle.gnm1.ann1 Main: 27317 90 16290 1629 1296.4 phavu.UI111.gnm1.ann1 Extra: 27146 96 16290 1614 1274.7 phavu.G19833.gnm1.ann1 Avg: 28053 89 16161 1614 1273 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 25747 99 21855 1677 1345.8 23_syn_pan_pctl25_posn_cds.fna == Proportion of initial genes retained in the "aug_extra" and "pctl25" sets: Start End_all End_core Pct_kept_all Pct_kept_core Annotation_name 27506 23908 22802 86.9 82.9 phaac.Frijol_Bayo.gnm1.ann1 27062 23120 22111 85.4 81.7 phaac.W6_15578.gnm2.ann1 29381 24627 24022 83.8 81.8 phaco.PHA8298.gnm1.ann1 32525 23022 22008 70.8 67.7 phalu.G27455.gnm1.ann1 27008 25521 25008 94.5 92.6 phavu.5-593.gnm1.ann1 27146 25430 25351 93.7 93.4 phavu.G19833.gnm1.ann1 27383 24954 24731 91.1 90.3 phavu.G19833.gnm2.ann1 27152 25740 25062 94.8 92.3 phavu.LaborOvalle.gnm1.ann1 27317 25711 25082 94.1 91.8 phavu.UI111.gnm1.ann1 == For all annotation sets, counts of genes-in-orthogroups and counts of orthogroups-with-genes: gns-in-OGs OGs-w-gns OGs-w-gns/gns pct-non-null-OGs pct-null-OGs annot-set 23908 23366 97.73 80.89 19.11 phaac.Frijol_Bayo.gnm1.ann1 23120 22656 97.99 78.44 21.56 phaac.W6_15578.gnm2.ann1 24627 23621 95.92 81.78 18.22 phaco.PHA8298.gnm1.ann1 23022 22335 97.02 77.32 22.68 phalu.G27455.gnm1.ann1 25521 24709 96.82 85.54 14.46 phavu.5-593.gnm1.ann1 25430 24537 96.49 84.95 15.05 phavu.G19833.gnm1.ann1 24954 24277 97.29 84.05 15.95 phavu.G19833.gnm2.ann1 25740 24847 96.53 86.02 13.98 phavu.LaborOvalle.gnm1.ann1 25711 24939 97.00 86.34 13.66 phavu.UI111.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 2133 3 1008 4 763 5 768 6 1282 7 3814 8 16455 9 331 10 140 11 111 12 99 13 61 14 65 15 28 16 12 17 8 18 6 19 5 20 1 22 2 24 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 3076 3 1322 4 945 5 867 6 1339 7 3863 8 16493 9 351 10 152 11 121 12 111 13 62 14 77 15 32 16 15 17 10 18 9 19 8 20 6 21 4 22 2 23 3 24 1 25 3 26 1 27 2 30 1 32 1 34 1 39 2 40 1 43 1 45 1 52 1 71 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 2359 3 1477 4 901 5 760 6 831 7 1328 8 3920 9 16255 10 386 11 151 12 115 13 88 14 90 15 54 16 68 17 17 18 24 19 12 20 8 21 7 22 6 23 2 24 3 25 1 26 2 27 2 28 4 29 1 31 3 32 1 37 1 40 1 41 2 46 1 50 1 51 1 57 1 74 1