Run of program pandagma pan, version 2023-01-28 Run started at: Sat Feb 3 08:50:54 AM CST 2024 Run ended at: Sat Feb 3 09:31:24 AM 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 Medicago.pan2 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method reference preferred_annot A17.gnm5.ann1_6 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 47728 largest_cluster 16 modal_clst_size 2 num_at_mode 12296 seqs_clustered 226603 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 55062 largest_cluster 102 modal_clst_size 2 num_at_mode 16988 seqs_clustered 246979 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 6 genes per OG (>= 23 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 55062 largest_cluster 2128 modal_clst_size>=6 23 num_at_mode>=6 8088 seqs_clustered 908377 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 40745 150 18939 1521 1173.4 medsa.XinJiangDaYe_hap1.gnm1.ann1 Main: 41399 150 15978 1521 1171.4 medsa.XinJiangDaYe_hap2.gnm1.ann1 Main: 41228 150 44046 1512 1172.4 medsa.XinJiangDaYe_hap3.gnm1.ann1 Main: 40414 150 16056 1518 1172.3 medsa.XinJiangDaYe_hap4.gnm1.ann1 Main: 50010 51 16158 1461 995.4 medtr.A17_HM341.gnm4.ann2 Main: 44425 123 16089 1476 1018.5 medtr.A17.gnm5.ann1_6 Main: 37351 201 16161 1590 1229.1 medtr.HM078.gnm1.ann1 Main: 38767 150 15306 1482 1105.4 medtr.R108.gnmHiC_1.ann1 Extra: 61422 30 15306 1452 992.1 medtr.HM004.gnm1.ann1 Extra: 62074 31 15306 1458 995.5 medtr.HM010.gnm1.ann1 Extra: 57064 30 16206 1455 993.9 medtr.HM022.gnm1.ann1 Extra: 61385 30 15306 1440 983.0 medtr.HM023.gnm1.ann1 Extra: 61476 31 15306 1464 994.4 medtr.HM034.gnm1.ann1 Extra: 62408 31 15306 1455 997.3 medtr.HM050.gnm1.ann1 Extra: 62388 31 16158 1461 992.8 medtr.HM056.gnm1.ann1 Extra: 61225 30 16209 1434 980.6 medtr.HM058.gnm1.ann1 Extra: 61528 31 15306 1455 991.3 medtr.HM060.gnm1.ann1 Extra: 62373 30 15306 1452 990.4 medtr.HM095.gnm1.ann1 Extra: 63357 32 15306 1470 996.9 medtr.HM125.gnm1.ann1 Extra: 62310 31 16206 1461 998.5 medtr.HM129.gnm1.ann1 Extra: 62470 31 15306 1458 995.5 medtr.HM185.gnm1.ann1 Extra: 57830 30 16644 1413 963.9 medtr.HM324.gnm1.ann1 Extra: 55416 9 15882 1293 831.4 medtr.R108_HM340.gnm1.ann1 Avg: 54307 67 17121 1465 1031 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 38541 96 15306 1545 1188.8 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 40745 30011 20273 73.7 49.8 medsa.XinJiangDaYe_hap1.gnm1.ann1 41399 30412 20516 73.5 49.6 medsa.XinJiangDaYe_hap2.gnm1.ann1 41228 30314 20302 73.5 49.2 medsa.XinJiangDaYe_hap3.gnm1.ann1 40414 29579 19905 73.2 49.3 medsa.XinJiangDaYe_hap4.gnm1.ann1 44425 34799 32956 78.3 74.2 medtr.A17.gnm5.ann1_6 50010 33183 32318 66.4 64.6 medtr.A17_HM341.gnm4.ann2 61422 44378 44026 72.3 71.7 medtr.HM004.gnm1.ann1 62074 45019 44738 72.5 72.1 medtr.HM010.gnm1.ann1 57064 41872 41031 73.4 71.9 medtr.HM022.gnm1.ann1 61385 44650 44277 72.7 72.1 medtr.HM023.gnm1.ann1 61476 44659 44390 72.6 72.2 medtr.HM034.gnm1.ann1 62408 44958 44665 72.0 71.6 medtr.HM050.gnm1.ann1 62388 45083 44637 72.3 71.5 medtr.HM056.gnm1.ann1 61225 44185 43702 72.2 71.4 medtr.HM058.gnm1.ann1 61528 44712 44420 72.7 72.2 medtr.HM060.gnm1.ann1 37351 31114 30040 83.3 80.4 medtr.HM078.gnm1.ann1 62373 45213 44942 72.5 72.1 medtr.HM095.gnm1.ann1 63357 45787 45323 72.3 71.5 medtr.HM125.gnm1.ann1 62310 45266 44962 72.6 72.2 medtr.HM129.gnm1.ann1 62470 45217 44925 72.4 71.9 medtr.HM185.gnm1.ann1 57830 41580 40608 71.9 70.2 medtr.HM324.gnm1.ann1 38767 27567 26766 71.1 69.0 medtr.R108.gnmHiC_1.ann1 55416 38819 36760 70.1 66.3 medtr.R108_HM340.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 30011 27668 92.19 50.25 49.75 medsa.XinJiangDaYe_hap1.gnm1.ann1 30412 27812 91.45 50.51 49.49 medsa.XinJiangDaYe_hap2.gnm1.ann1 30314 27486 90.67 49.92 50.08 medsa.XinJiangDaYe_hap3.gnm1.ann1 29579 27020 91.35 49.07 50.93 medsa.XinJiangDaYe_hap4.gnm1.ann1 34799 34147 98.13 62.02 37.98 medtr.A17.gnm5.ann1_6 33183 32529 98.03 59.08 40.92 medtr.A17_HM341.gnm4.ann2 44378 35318 79.58 64.14 35.86 medtr.HM004.gnm1.ann1 45019 35501 78.86 64.47 35.53 medtr.HM010.gnm1.ann1 41872 34047 81.31 61.83 38.17 medtr.HM022.gnm1.ann1 44650 35518 79.55 64.51 35.49 medtr.HM023.gnm1.ann1 44659 35295 79.03 64.10 35.90 medtr.HM034.gnm1.ann1 44958 35442 78.83 64.37 35.63 medtr.HM050.gnm1.ann1 45083 35570 78.90 64.60 35.40 medtr.HM056.gnm1.ann1 44185 35611 80.60 64.67 35.33 medtr.HM058.gnm1.ann1 44712 35485 79.36 64.45 35.55 medtr.HM060.gnm1.ann1 31114 30586 98.30 55.55 44.45 medtr.HM078.gnm1.ann1 45213 35422 78.34 64.33 35.67 medtr.HM095.gnm1.ann1 45787 35517 77.57 64.50 35.50 medtr.HM125.gnm1.ann1 45266 35481 78.38 64.44 35.56 medtr.HM129.gnm1.ann1 45217 35350 78.18 64.20 35.80 medtr.HM185.gnm1.ann1 41580 33829 81.36 61.44 38.56 medtr.HM324.gnm1.ann1 27567 26983 97.88 49.00 51.00 medtr.R108.gnmHiC_1.ann1 38819 31661 81.56 57.50 42.50 medtr.R108_HM340.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 12296 3 7275 4 7609 5 1900 6 2722 7 5240 8 9536 9 825 10 185 11 74 12 32 13 12 14 11 15 9 16 2 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 16988 3 8716 4 8220 5 2170 6 2851 7 5310 8 9567 9 846 10 202 11 81 12 36 13 20 14 16 15 13 16 7 17 6 18 1 19 1 20 2 22 1 23 3 41 1 42 1 51 1 59 1 102 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 6235 3 4280 4 3603 5 1485 6 985 7 728 8 676 9 548 10 550 11 552 12 577 13 665 14 807 15 995 16 1474 17 1717 18 2087 19 3480 20 1953 21 2653 22 4832 23 8088 24 1772 25 653 26 382 27 327 28 279 29 242 30 220 31 205 32 159 33 168 34 144 35 136 36 113 37 75 38 81 39 75 40 52 41 66 42 57 43 33 44 45 45 38 46 30 47 28 48 31 49 25 50 13 51 17 52 22 53 21 54 16 55 15 56 19 57 14 58 23 59 7 60 9 61 18 62 12 63 12 64 7 65 12 66 9 67 7 68 3 69 10 70 6 71 12 72 10 73 10 74 10 75 4 76 3 77 4 78 5 79 8 80 7 81 3 82 5 83 3 84 4 85 4 86 6 87 7 88 5 89 4 90 4 91 4 92 3 93 4 94 2 95 4 96 3 97 2 98 3 99 5 100 3 101 6 102 3 103 3 104 6 105 3 106 2 107 3 108 2 109 2 110 1 111 9 112 5 113 2 114 5 117 2 118 2 119 3 120 2 121 5 123 2 124 2 125 1 126 6 127 2 128 1 130 1 131 1 133 5 134 2 135 2 138 2 142 2 143 1 144 1 145 1 149 1 150 2 151 2 152 1 154 1 155 1 156 1 157 1 158 2 159 1 160 1 163 1 164 1 165 1 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