Run of program pandagma pan, version 2026-01-28 Run started at: Thu Jan 29 11:36:44 CST 2026 Run ended at: Thu Jan 29 13:47:08 CST 2026 Sequence type: nucleotide Parameter value clust_iden 0.80 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.pan4 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 32755 largest_cluster 41 modal_clst_size 13 num_at_mode 8734 seqs_clustered 312111 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 32755 largest_cluster 95 modal_clst_size 13 num_at_mode 9602 seqs_clustered 334300 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 4 genes per OG (>= 13 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 32755 largest_cluster 96 modal_clst_size>=4 13 num_at_mode>=4 9131 seqs_clustered 332778 == 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: 31932 90 16278 1602 1215.3 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 Main: 26739 18 17061 1581 1171.9 vigan.Gyeongwon.gnm3.ann1 Main: 31147 150 16263 1521 1080.5 vigan.Shumari.gnm1.ann1 Main: 22359 12 15450 1614 1264.5 vigra.VC1973A.gnm6.ann1 Main: 30957 6 13857 1473 1081.7 vigra.VC1973A.gnm7.ann1 Main: 28739 153 31758 1617 1260.3 vigra.Weilv-9.gnm1.ann1 Main: 29773 90 16278 1611 1238.7 vigun.IT97K-499-35.gnm1.ann1 Avg: 28530 81 17269 1587 1213 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 26822 90 20616 1650 1288.5 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 18397 17085 68.8 63.9 vigan.Gyeongwon.gnm3.ann1 31147 23014 21896 73.9 70.3 vigan.Shumari.gnm1.ann1 22359 18484 16726 82.7 74.8 vigra.VC1973A.gnm6.ann1 30957 22539 20096 72.8 64.9 vigra.VC1973A.gnm7.ann1 28739 25401 23216 88.4 80.8 vigra.Weilv-9.gnm1.ann1 28284 27443 26921 97.0 95.2 vigun.CB5-2.gnm1.ann1 29773 28250 27647 94.9 92.9 vigun.IT97K-499-35.gnm1.ann1 31932 30277 29303 94.8 91.8 vigun.IT97K-499-35.gnm1.ann2 28444 27919 27315 98.2 96.0 vigun.Sanzi.gnm1.ann1 28529 28043 27431 98.3 96.2 vigun.Suvita2.gnm1.ann1 27734 27524 27019 99.2 97.4 vigun.TZ30.gnm1.ann2 28550 27962 27294 97.9 95.6 vigun.UCR779.gnm1.ann1 27715 27525 26989 99.3 97.4 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 18397 17699 96.21 54.03 45.97 vigan.Gyeongwon.gnm3.ann1 23014 21569 93.72 65.85 34.15 vigan.Shumari.gnm1.ann1 18484 17777 96.18 54.27 45.73 vigra.VC1973A.gnm6.ann1 22539 20408 90.55 62.30 37.70 vigra.VC1973A.gnm7.ann1 25401 23287 91.68 71.09 28.91 vigra.Weilv-9.gnm1.ann1 27443 25802 94.02 78.77 21.23 vigun.CB5-2.gnm1.ann1 28250 25164 89.08 76.82 23.18 vigun.IT97K-499-35.gnm1.ann1 30277 26605 87.87 81.22 18.78 vigun.IT97K-499-35.gnm1.ann2 27919 26153 93.67 79.84 20.16 vigun.Sanzi.gnm1.ann1 28043 26259 93.64 80.17 19.83 vigun.Suvita2.gnm1.ann1 27524 25800 93.74 78.77 21.23 vigun.TZ30.gnm1.ann2 27962 26080 93.27 79.62 20.38 vigun.UCR779.gnm1.ann1 27525 25806 93.75 78.78 21.22 vigun.ZN016.gnm1.ann2 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 4336 3 1839 4 1112 5 1028 6 719 7 893 8 1590 9 831 10 1646 11 3196 12 5414 13 8734 14 257 15 148 16 99 17 90 18 92 19 81 20 85 21 95 22 67 23 74 24 82 25 105 26 106 27 7 28 3 29 7 30 4 31 4 32 5 33 2 35 1 36 1 39 1 41 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 2907 3 1756 4 1212 5 1121 6 759 7 920 8 1750 9 798 10 1451 11 2811 12 5175 13 9602 14 580 15 304 16 196 17 142 18 116 19 125 20 126 21 155 22 93 23 111 24 99 25 126 26 167 27 21 28 15 29 14 30 12 31 15 32 12 33 10 34 7 35 6 36 2 37 5 38 5 39 2 40 2 41 3 42 4 43 1 44 2 45 2 50 1 51 2 53 1 54 2 56 1 57 2 61 1 73 1 88 1 95 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 3086 3 1738 4 1163 5 1066 6 713 7 968 8 1730 9 795 10 1506 11 3004 12 5420 13 9131 14 535 15 275 16 195 17 136 18 123 19 123 20 133 21 159 22 100 23 114 24 102 25 123 26 164 27 13 28 23 29 10 30 20 31 8 32 14 33 12 34 5 35 4 36 6 37 2 38 6 39 3 40 2 41 4 42 2 43 3 44 1 45 2 50 2 51 1 53 2 55 1 56 3 59 1 72 1 88 1 96 1