Run of program pandagma pan, version 2025-05-30 Run started at: Wed Aug 6 15:39:09 CDT 2025 Run ended at: Wed Aug 6 17:23:07 CDT 2025 Sequence type: nucleotide Parameter value clust_iden 0.90 clust_cov 0.50 extra_iden 0.70 mcl_inflation 1.6 strict_synt 1 pctl_low 25 pctl_med 50 pctl_hi 75 consen_prefix Zea.pan4 annot_str_regex (\D+\d+\D+)\d+.+ order_method reference preferred_annot Zm00001eb 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 85842 largest_cluster 156 modal_clst_size 2 num_at_mode 24299 seqs_clustered 1218987 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 97202 largest_cluster 156 modal_clst_size 2 num_at_mode 30436 seqs_clustered 1264006 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 17 genes per OG (>= 66 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 97202 largest_cluster 315 modal_clst_size>=17 64 num_at_mode>=17 4156 seqs_clustered 2280569 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 70394 66 16278 1386 1005.8 Zd-Gigi-REFERENCE-PanAnd-1. Main: 58214 66 16278 1392 1002.5 Zd-Momo-REFERENCE-PanAnd-1. Main: 55314 72 16278 1353 975.7 Zh-RIMHU001-REFERENCE-PanAnd- Main: 39744 87 16278 1437 1088.8 Zm-B73-REFERENCE-NAM- Main: 49202 9 15804 1443 1053.7 Zm-B73-REFERENCE-GRAMENE- Main: 40368 135 16278 1434 1077.9 Zm-B97-REFERENCE-NAM- Main: 40013 93 16278 1434 1080.6 Zm-CML103-REFERENCE-NAM- Main: 41577 45 16278 1422 1076.0 Zm-CML228-REFERENCE-NAM- Main: 40383 84 15201 1431 1082.4 Zm-CML247-REFERENCE-NAM- Main: 40325 105 16278 1431 1077.7 Zm-CML277-REFERENCE-NAM- Main: 41122 105 16278 1422 1067.0 Zm-CML322-REFERENCE-NAM- Main: 40428 72 16278 1431 1080.3 Zm-CML333-REFERENCE-NAM- Main: 40473 126 16278 1428 1087.6 Zm-CML52-REFERENCE-NAM- Main: 40272 120 16278 1422 1062.3 Zm-CML69-REFERENCE-NAM- Main: 39785 69 16278 1431 1085.4 Zm-HP301-REFERENCE-NAM- Main: 40290 69 16278 1425 1074.6 Zm-Il14H-REFERENCE-NAM- Main: 39868 156 16278 1437 1087.1 Zm-Ki11-REFERENCE-NAM- Main: 41059 138 16278 1422 1071.8 Zm-Ki3-REFERENCE-NAM- Main: 40778 123 16278 1425 1070.0 Zm-Ky21-REFERENCE-NAM- Main: 41486 105 16278 1416 1062.2 Zm-M162W-REFERENCE-NAM- Main: 40905 138 16278 1428 1071.6 Zm-M37W-REFERENCE-NAM- Main: 41204 75 16278 1419 1061.1 Zm-Mo18W-REFERENCE-NAM- Main: 41247 69 16278 1422 1074.6 Zm-Ms71-REFERENCE-NAM- Main: 40484 153 16278 1434 1082.6 Zm-NC350-REFERENCE-NAM- Main: 39787 117 16278 1437 1086.2 Zm-NC358-REFERENCE-NAM- Main: 39973 156 16278 1437 1082.7 Zm-Oh43-REFERENCE-NAM- Main: 40334 105 16278 1431 1078.0 Zm-Oh7B-REFERENCE-NAM- Main: 41478 99 16278 1416 1059.2 Zm-P39-REFERENCE-NAM- Main: 41164 132 16278 1419 1065.5 Zm-Tx303-REFERENCE-NAM- Main: 41593 27 16278 1419 1066.0 Zm-Tzi8-REFERENCE-NAM- Main: 62715 54 16278 1338 963.2 Zn-PI615697-REFERENCE-PanAnd- Main: 54839 48 16278 1347 970.3 Zv-TIL01-REFERENCE-PanAnd- Main: 53979 48 16278 1350 972.5 Zv-TIL11-REFERENCE-PanAnd- Main: 52070 54 16278 1362 989.4 Zx-TIL18-REFERENCE-PanAnd- Main: 52432 51 16458 1362 983.2 Zx-TIL25-REFERENCE-PanAnd- Extra: 110151 18 14668 1513 903.4 Zm-B73-REFERENCE-GRAMENE- Extra: 40747 93 16392 1485 1089.7 Zm-A188-REFERENCE-KSU- Extra: 45287 150 16269 1485 1122.0 Zm-A632-REFERENCE-CAAS_FIL- Extra: 42500 150 15201 1494 1140.9 Zm-Chang-7_ Extra: 40104 9 16278 1275 973.3 Zm-CML457-REFERENCE-HiLo- Extra: 39298 15 16278 1446 1114.3 Zm-CML459-REFERENCE-HiLo- Extra: 42075 12 16278 1542 1183.1 Zm-CML530-REFERENCE-HiLo- Extra: 43718 150 16278 1485 1124.0 Zm-Dan340-REFERENCE-CAAS_FIL- Extra: 48140 30 16278 1389 998.2 Zm-DK105-REFERENCE-TUM- Extra: 44852 24 17034 1973 1419.4 Zm-EA1197-REFERENCE-AMZ- Extra: 46105 30 16278 1404 1025.2 Zm-EP1-REFERENCE-TUM- Extra: 48370 30 16278 1383 999.6 Zm-F7-REFERENCE-TUM- Extra: 44771 6 16278 1488 1125.8 Zm-Huangzaosi-REFERENCE-CAAS_FIL-1. Extra: 38368 48 19343 2178 1635.7 Zm-Ia453-REFERENCE-FL- Extra: 46311 62 16278 1473 1111.9 Zm-Jing724-REFERENCE-CAAS_FIL- Extra: 45537 150 16278 1479 1120.2 Zm-Jing92-REFERENCE-CAAS_FIL- Extra: 38238 156 15465 1476 1126.0 Zm-K0326Y-REFERENCE-SIPPE- Extra: 42580 75 15201 1473 1094.2 Zm-Mo17-REFERENCE-CAU- Extra: 52317 51 16809 1431 1132.1 Zm-PDJ-REFERENCE-HiLo-1. Extra: 48306 30 16278 1389 998.0 Zm-PE0075-REFERENCE-TUM- Extra: 45809 150 16278 1458 1104.9 Zm-PH207-REFERENCE-CAAS_FIL- Extra: 40557 9 14844 1404 1061.4 Zm-PH207-REFERENCE_NS-UIUC_UMN- Extra: 40357 51 16278 1518 1213.5 Zm-PT-REFERENCE-HiLo-1. Extra: 44719 150 16302 1479 1124.6 Zm-S37-REFERENCE-CAAS_FIL- Extra: 43271 120 16278 1530 1179.3 Zm-SK-REFERENCE-YAN-1. Extra: 48487 66 16278 1500 1180.9 Zm-TAB-REFERENCE-HiLo-1. Extra: 40690 6 16281 1491 1141.3 Zm-W22-REFERENCE-NRGENE- Extra: 44191 150 16278 1482 1119.8 Zm-Xu178-REFERENCE-CAAS_FIL- Extra: 44791 150 16278 1482 1120.8 Zm-Ye478-REFERENCE-CAAS_FIL- Extra: 44482 24 16278 1374 1034.3 Zm-ZAP-REFERENCE-HiLo-1. Extra: 44845 150 16269 1482 1121.0 Zm-Zheng58-REFERENCE-CAAS_FIL- Avg: 45382 83 16233 1453 1086 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 34734 111 16278 1527 1202.4 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 46671 35076 27156 75.2 58.2 >Zm00001ca 70394 37493 29171 53.3 41.4 Zd00001ab 58214 36963 29713 63.5 51.0 Zd00003ab 55314 32473 27165 58.7 49.1 Zh00001ab 63480 34389 29030 54.2 45.7 Zm00001ca 49202 36057 29992 73.3 61.0 Zm00001d 39744 33137 28645 83.4 72.1 Zm00001eb 40690 28239 25114 69.4 61.7 Zm00004b 40557 34515 30824 85.1 76.0 Zm00008a 46105 34728 30899 75.3 67.0 Zm00010a 48370 32473 28971 67.1 59.9 Zm00011a 42580 32060 28280 75.3 66.4 Zm00014ba 43271 35460 30719 81.9 71.0 Zm00015a 48140 35750 31076 74.3 64.6 Zm00016a 48306 36884 30245 76.4 62.6 Zm00017a 40368 34597 29474 85.7 73.0 Zm00018ab 40473 35466 29598 87.6 73.1 Zm00019ab 40272 35781 29998 88.8 74.5 Zm00020ab 40013 35724 29885 89.3 74.7 Zm00021ab 41577 36003 30028 86.6 72.2 Zm00022ab 40383 35711 29934 88.4 74.1 Zm00023ab 40325 36043 30100 89.4 74.6 Zm00024ab 41122 35856 30028 87.2 73.0 Zm00025ab 40428 35707 29936 88.3 74.0 Zm00026ab 39785 35860 29918 90.1 75.2 Zm00027ab 40290 36168 30122 89.8 74.8 Zm00028ab 41059 35824 30137 87.3 73.4 Zm00029ab 39868 36590 30253 91.8 75.9 Zm00030ab 40778 36437 30223 89.4 74.1 Zm00031ab 40905 36343 30147 88.8 73.7 Zm00032ab 41486 36351 30134 87.6 72.6 Zm00033ab 41204 36359 30141 88.2 73.2 Zm00034ab 41247 36152 30183 87.6 73.2 Zm00035ab 40484 36055 30148 89.1 74.5 Zm00036ab 39787 36217 30093 91.0 75.6 Zm00037ab 40334 36012 30089 89.3 74.6 Zm00038ab 39973 36136 29944 90.4 74.9 Zm00039ab 41478 36447 30237 87.9 72.9 Zm00040ab 41164 36198 30149 87.9 73.2 Zm00041ab 41593 20848 18311 50.1 44.0 Zm00042ab 38368 27591 24119 71.9 62.9 Zm00045a 38238 32052 28343 83.8 74.1 Zm00054a 40747 25312 21581 62.1 53.0 Zm00056aa 44852 35141 31347 78.3 69.9 Zm00063aa 45287 33172 30122 73.2 66.5 Zm00092aa 42500 33310 29997 78.4 70.6 Zm00093aa 43718 34520 31078 79.0 71.1 Zm00094aa 44771 35070 31216 78.3 69.7 Zm00095aa 46311 35137 31530 75.9 68.1 Zm00096aa 45537 35103 31196 77.1 68.5 Zm00097aa 45809 34147 30571 74.5 66.7 Zm00099aa 44719 33766 30243 75.5 67.6 Zm00100aa 44191 34262 30583 77.5 69.2 Zm00101aa 44791 34592 31026 77.2 69.3 Zm00102aa 44845 30134 25887 67.2 57.7 Zm00103aa 40104 33508 29662 83.6 74.0 Zm00106aa 39298 33698 29944 85.7 76.2 Zm00107aa 42075 31622 28011 75.2 66.6 Zm00108aa 40357 35629 30392 88.3 75.3 Zm00109aa 44482 33738 28468 75.8 64.0 Zm00110aa 48487 35376 29615 73.0 61.1 Zm00111aa 52317 26861 21825 51.3 41.7 Zm00112aa 62715 39794 30826 63.5 49.2 Zn00001ab 54839 40007 30856 73.0 56.3 Zv00001ab 53979 38143 30245 70.7 56.0 Zv00002ab 52070 38302 30200 73.6 58.0 Zx00002ab 52432 0 0 0.0 0.0 Zx00003ab == 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 35076 33246 94.78 34.20 65.80 Zd00001ab 37493 34595 92.27 35.59 64.41 Zd00003ab 36963 34620 93.66 35.62 64.38 Zh00001ab 32473 29380 90.48 30.23 69.77 Zm00001ca 34389 33066 96.15 34.02 65.98 Zm00001d 36057 35009 97.09 36.02 63.98 Zm00001eb 33137 30884 93.20 31.77 68.23 Zm00004b 28239 27148 96.14 27.93 72.07 Zm00008a 34515 32912 95.36 33.86 66.14 Zm00010a 34728 33055 95.18 34.01 65.99 Zm00011a 32473 31066 95.67 31.96 68.04 Zm00014ba 32060 30811 96.10 31.70 68.30 Zm00015a 35460 33183 93.58 34.14 65.86 Zm00016a 35750 33449 93.56 34.41 65.59 Zm00017a 36884 35938 97.44 36.97 63.03 Zm00018ab 34597 33619 97.17 34.59 65.41 Zm00019ab 35466 34530 97.36 35.52 64.48 Zm00020ab 35781 34868 97.45 35.87 64.13 Zm00021ab 35724 34766 97.32 35.77 64.23 Zm00022ab 36003 35075 97.42 36.08 63.92 Zm00023ab 35711 34810 97.48 35.81 64.19 Zm00024ab 36043 35072 97.31 36.08 63.92 Zm00025ab 35856 34897 97.33 35.90 64.10 Zm00026ab 35707 34816 97.50 35.82 64.18 Zm00027ab 35860 34879 97.26 35.88 64.12 Zm00028ab 36168 35244 97.45 36.26 63.74 Zm00029ab 35824 34860 97.31 35.86 64.14 Zm00030ab 36590 35636 97.39 36.66 63.34 Zm00031ab 36437 35436 97.25 36.46 63.54 Zm00032ab 36343 35320 97.19 36.34 63.66 Zm00033ab 36351 35375 97.32 36.39 63.61 Zm00034ab 36359 35373 97.29 36.39 63.61 Zm00035ab 36152 35136 97.19 36.15 63.85 Zm00036ab 36055 35121 97.41 36.13 63.87 Zm00037ab 36217 35306 97.48 36.32 63.68 Zm00038ab 36012 35119 97.52 36.13 63.87 Zm00039ab 36136 35090 97.11 36.10 63.90 Zm00040ab 36447 35432 97.22 36.45 63.55 Zm00041ab 36198 35212 97.28 36.23 63.77 Zm00042ab 20848 20138 96.59 20.72 79.28 Zm00045a 27591 26199 94.95 26.95 73.05 Zm00054a 32052 29917 93.34 30.78 69.22 Zm00056aa 25312 23222 91.74 23.89 76.11 Zm00063aa 35141 33166 94.38 34.12 65.88 Zm00092aa 33172 31493 94.94 32.40 67.60 Zm00093aa 33310 31648 95.01 32.56 67.44 Zm00094aa 34520 32615 94.48 33.55 66.45 Zm00095aa 35070 33181 94.61 34.14 65.86 Zm00096aa 35137 33310 94.80 34.27 65.73 Zm00097aa 35103 33271 94.78 34.23 65.77 Zm00099aa 34147 32208 94.32 33.14 66.86 Zm00100aa 33766 32034 94.87 32.96 67.04 Zm00101aa 34262 32530 94.94 33.47 66.53 Zm00102aa 34592 32857 94.98 33.80 66.20 Zm00103aa 30134 27964 92.80 28.77 71.23 Zm00106aa 33508 31440 93.83 32.35 67.65 Zm00107aa 33698 31507 93.50 32.41 67.59 Zm00108aa 31622 29558 93.47 30.41 69.59 Zm00109aa 35629 33115 92.94 34.07 65.93 Zm00110aa 33738 30475 90.33 31.35 68.65 Zm00111aa 35376 31858 90.06 32.78 67.22 Zm00112aa 26861 25078 93.36 25.80 74.20 Zn00001ab 39794 37578 94.43 38.66 61.34 Zv00001ab 40007 37855 94.62 38.94 61.06 Zv00002ab 38143 36150 94.77 37.19 62.81 Zx00002ab 38302 36247 94.63 37.29 62.71 Zx00003ab Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 6 2 24299 3 9980 4 5602 5 3728 6 2799 7 2056 8 1759 9 1387 10 1032 11 882 12 775 13 602 14 560 15 465 16 442 17 410 18 347 19 360 20 299 21 307 22 299 23 305 24 260 25 269 26 317 27 315 28 342 29 387 30 531 31 721 32 1242 33 2617 34 6791 35 10297 36 1163 37 354 38 187 39 144 40 125 41 116 42 96 43 97 44 58 45 58 46 43 47 35 48 39 49 34 50 30 51 32 52 28 53 36 54 25 55 22 56 21 57 13 58 21 59 14 60 15 61 20 62 13 63 15 64 10 65 19 66 14 67 12 68 17 69 10 70 8 71 5 72 7 73 6 74 6 75 2 76 5 77 5 78 6 79 4 80 2 81 2 82 4 83 2 84 5 85 4 86 1 87 1 89 1 90 2 91 4 92 1 93 3 94 2 95 2 97 2 98 3 99 3 100 2 101 1 102 1 104 3 111 1 113 1 114 1 117 1 125 1 128 1 135 2 140 1 145 1 156 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 6 2 30436 3 12043 4 6707 5 4308 6 3158 7 2269 8 1914 9 1521 10 1115 11 940 12 822 13 652 14 597 15 498 16 465 17 431 18 364 19 381 20 314 21 318 22 308 23 316 24 274 25 278 26 327 27 323 28 353 29 396 30 541 31 731 32 1252 33 2636 34 6798 35 10313 36 1166 37 354 38 189 39 146 40 125 41 117 42 98 43 97 44 59 45 59 46 45 47 35 48 39 49 34 50 32 51 33 52 28 53 38 54 29 55 22 56 22 57 14 58 21 59 14 60 16 61 20 62 14 63 15 64 10 65 20 66 14 67 12 68 17 69 11 70 9 71 6 72 7 73 6 74 6 75 2 76 5 77 6 78 6 79 4 80 2 81 2 82 5 83 2 84 7 85 4 86 1 87 1 89 1 90 2 91 4 92 2 93 3 94 2 95 2 97 2 98 3 99 3 100 2 101 1 102 2 104 3 107 1 111 1 112 1 113 1 114 1 117 1 119 1 121 1 123 1 125 1 128 1 135 2 137 1 140 2 145 1 146 1 156 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 5 2 17882 3 10018 4 6841 5 5048 6 3930 7 3261 8 2745 9 2394 10 1858 11 1612 12 1461 13 1217 14 1098 15 890 16 844 17 798 18 657 19 647 20 592 21 525 22 475 23 457 24 414 25 362 26 363 27 306 28 303 29 292 30 236 31 214 32 216 33 238 34 196 35 159 36 204 37 201 38 165 39 160 40 157 41 146 42 148 43 143 44 170 45 168 46 168 47 147 48 196 49 178 50 183 51 185 52 241 53 222 54 305 55 341 56 395 57 542 58 675 59 926 60 1343 61 1989 62 2674 63 3628 64 4156 65 3681 66 2195 67 679 68 281 69 173 70 143 71 129 72 109 73 86 74 63 75 54 76 52 77 48 78 29 79 32 80 33 81 21 82 28 83 27 84 19 85 20 86 14 87 15 88 18 89 13 90 9 91 22 92 14 93 13 94 12 95 11 96 13 97 14 98 13 99 9 100 14 101 15 102 7 103 11 104 12 105 8 106 7 107 5 108 5 109 12 110 9 111 9 112 7 113 7 114 9 115 7 116 4 117 11 118 8 119 6 120 8 121 6 122 13 123 7 124 16 125 6 126 10 127 7 128 9 129 5 130 4 131 8 132 6 133 7 134 2 135 4 136 2 137 4 138 1 139 1 140 4 141 2 142 5 143 1 144 3 145 4 146 2 147 2 148 3 149 4 150 1 153 4 154 4 155 2 156 1 157 1 158 1 159 2 160 2 161 1 162 1 163 3 165 1 168 1 170 1 171 1 172 1 174 1 177 3 179 2 180 2 181 1 182 3 185 1 186 2 188 1 196 1 198 1 199 1 200 1 201 1 208 1 209 2 212 1 217 1 218 1 220 1 222 1 230 1 231 2 232 1 235 1 243 1 245 1 255 1 268 1 279 1 280 2 301 1 315 1