Run of program pandagma pan, version 2023-01-28 Run started at: Wed Jan 31 08:31:06 PM CST 2024 Run ended at: Wed Jan 31 08:58:24 PM CST 2024 Sequence type: nucleotide Parameter value clust_iden 0.95 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 Vigna.pan3 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method alignment preferred_annot IT97K-499-35.gnm1.ann2 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 29488 largest_cluster 15 modal_clst_size 7 num_at_mode 22993 seqs_clustered 187621 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 30165 largest_cluster 26 modal_clst_size 7 num_at_mode 23034 seqs_clustered 189835 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 4 genes per OG (>= 12 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 30165 largest_cluster 64 modal_clst_size>=4 12 num_at_mode>=4 13369 seqs_clustered 306344 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 28284 90 16188 1602 1240.3 vigun.CB5-2.gnm1.ann1 Main: 31939 90 16278 1602 1215.1 vigun.IT97K-499-35.gnm1.ann2 Main: 28444 90 16278 1602 1238.5 vigun.Sanzi.gnm1.ann1 Main: 28529 90 16272 1605 1239.9 vigun.Suvita2.gnm1.ann1 Main: 27734 90 16272 1602 1254.5 vigun.TZ30.gnm1.ann2 Main: 28550 90 16272 1602 1239.9 vigun.UCR779.gnm1.ann1 Main: 27715 90 16272 1605 1254.5 vigun.ZN016.gnm1.ann2 Extra: 29773 90 16278 1611 1238.7 vigun.IT97K-499-35.gnm1.ann1 Extra: 26739 18 17061 1581 1171.9 vigan.Gyeongwon.gnm3.ann1 Extra: 31147 150 16263 1521 1080.5 vigan.Shumari.gnm1.ann1 Extra: 22359 12 15450 1614 1264.5 vigra.VC1973A.gnm6.ann1 Extra: 30957 6 13857 1473 1081.7 vigra.VC1973A.gnm7.ann1 Avg: 28514 75 16061 1585 1210 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 28667 84 24465 1617 1260.6 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 26739 21562 21558 80.6 80.6 vigan.Gyeongwon.gnm3.ann1 31147 23183 23182 74.4 74.4 vigan.Shumari.gnm1.ann1 22359 19693 19692 88.1 88.1 vigra.VC1973A.gnm6.ann1 30957 24836 24834 80.2 80.2 vigra.VC1973A.gnm7.ann1 28284 27175 26843 96.1 94.9 vigun.CB5-2.gnm1.ann1 29773 27235 27134 91.5 91.1 vigun.IT97K-499-35.gnm1.ann1 31939 28132 27660 88.1 86.6 vigun.IT97K-499-35.gnm1.ann2 28444 26802 26490 94.2 93.1 vigun.Sanzi.gnm1.ann1 28529 27204 26859 95.4 94.1 vigun.Suvita2.gnm1.ann1 27734 26852 26528 96.8 95.7 vigun.TZ30.gnm1.ann2 28550 26853 26498 94.1 92.8 vigun.UCR779.gnm1.ann1 27715 26817 26482 96.8 95.6 vigun.ZN016.gnm1.ann2 == 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 21562 20319 94.24 67.36 32.64 vigan.Gyeongwon.gnm3.ann1 23183 21712 93.65 71.98 28.02 vigan.Shumari.gnm1.ann1 19693 18659 94.75 61.86 38.14 vigra.VC1973A.gnm6.ann1 24836 21719 87.45 72.00 28.00 vigra.VC1973A.gnm7.ann1 27175 27088 99.68 89.80 10.20 vigun.CB5-2.gnm1.ann1 27235 26335 96.70 87.30 12.70 vigun.IT97K-499-35.gnm1.ann1 28132 27623 98.19 91.57 8.43 vigun.IT97K-499-35.gnm1.ann2 26802 26728 99.72 88.61 11.39 vigun.Sanzi.gnm1.ann1 27204 27144 99.78 89.99 10.01 vigun.Suvita2.gnm1.ann1 26852 26777 99.72 88.77 11.23 vigun.TZ30.gnm1.ann2 26853 26781 99.73 88.78 11.22 vigun.UCR779.gnm1.ann1 26817 26761 99.79 88.72 11.28 vigun.ZN016.gnm1.ann2 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 1706 3 1046 4 910 5 1030 6 1631 7 22993 8 95 9 32 10 21 11 12 12 6 13 3 14 2 15 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 2085 3 1170 4 972 5 1055 6 1659 7 23034 8 100 9 34 10 21 11 12 12 7 13 4 14 3 15 3 16 1 18 1 21 1 24 2 26 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 1157 3 1039 4 824 5 796 6 753 7 943 8 1549 9 1176 10 2059 11 4330 12 13369 13 1121 14 525 15 204 16 153 17 55 18 34 19 18 20 15 21 11 22 5 23 5 24 4 25 3 26 3 27 4 29 1 33 1 35 1 37 1 44 1 46 1 55 2 63 1 64 1