Run of program pandagma pan, version 2025-12-30 Run started at: Mon Jan 26 20:43:07 CST 2026 Run ended at: Tue Jan 27 14:03:55 CST 2026 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.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 41253 largest_cluster 25 modal_clst_size 8 num_at_mode 8293 seqs_clustered 312712 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 41253 largest_cluster 99 modal_clst_size 8 num_at_mode 8540 seqs_clustered 324061 == 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 41253 largest_cluster 98 modal_clst_size>=4 8 num_at_mode>=4 8491 seqs_clustered 322363 == 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: 29187 90 59490 1755 1376.3 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 17431 15033 65.2 56.2 vigan.Gyeongwon.gnm3.ann1 31147 21658 18693 69.5 60.0 vigan.Shumari.gnm1.ann1 22359 17621 14814 78.8 66.3 vigra.VC1973A.gnm6.ann1 30957 20544 15899 66.4 51.4 vigra.VC1973A.gnm7.ann1 28739 23943 18960 83.3 66.0 vigra.Weilv-9.gnm1.ann1 28284 27244 26578 96.3 94.0 vigun.CB5-2.gnm1.ann1 29773 27563 26900 92.6 90.4 vigun.IT97K-499-35.gnm1.ann1 31932 29410 28317 92.1 88.7 vigun.IT97K-499-35.gnm1.ann2 28444 27516 26838 96.7 94.4 vigun.Sanzi.gnm1.ann1 28529 27639 26882 96.9 94.2 vigun.Suvita2.gnm1.ann1 27734 27201 26579 98.1 95.8 vigun.TZ30.gnm1.ann2 28550 27442 26692 96.1 93.5 vigun.UCR779.gnm1.ann1 27715 27151 26511 98.0 95.7 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 17431 17261 99.02 41.84 58.16 vigan.Gyeongwon.gnm3.ann1 21658 21192 97.85 51.37 48.63 vigan.Shumari.gnm1.ann1 17621 17446 99.01 42.29 57.71 vigra.VC1973A.gnm6.ann1 20544 19671 95.75 47.68 52.32 vigra.VC1973A.gnm7.ann1 23943 23298 97.31 56.48 43.52 vigra.Weilv-9.gnm1.ann1 27244 27055 99.31 65.58 34.42 vigun.CB5-2.gnm1.ann1 27563 26226 95.15 63.57 36.43 vigun.IT97K-499-35.gnm1.ann1 29410 27715 94.24 67.18 32.82 vigun.IT97K-499-35.gnm1.ann2 27516 27246 99.02 66.05 33.95 vigun.Sanzi.gnm1.ann1 27639 27388 99.09 66.39 33.61 vigun.Suvita2.gnm1.ann1 27201 26952 99.08 65.33 34.67 vigun.TZ30.gnm1.ann2 27442 27132 98.87 65.77 34.23 vigun.UCR779.gnm1.ann1 27151 26916 99.13 65.25 34.75 vigun.ZN016.gnm1.ann2 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 6325 3 3596 4 2663 5 2948 6 925 7 1354 8 8293 9 567 10 1207 11 2292 12 4209 13 6752 14 72 15 23 16 6 17 8 18 4 19 5 20 1 21 1 23 1 25 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 5274 3 3448 4 2748 5 3246 6 969 7 1321 8 8540 9 534 10 1156 11 2135 12 4046 13 7257 14 221 15 131 16 66 17 36 18 24 19 18 20 12 21 12 22 9 23 7 24 7 25 3 26 1 27 6 28 5 29 1 30 2 31 2 32 2 33 2 34 1 35 1 36 1 41 1 42 1 51 1 53 1 54 1 55 1 59 2 99 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 5471 3 3458 4 2775 5 3081 6 940 7 1364 8 8491 9 581 10 1151 11 2255 12 4170 13 6981 14 201 15 137 16 50 17 32 18 22 19 15 20 11 21 9 22 10 23 7 24 7 26 4 27 6 28 2 29 3 30 2 31 2 32 3 33 1 34 1 37 1 40 1 41 1 52 2 53 1 54 1 58 2 98 1