Run of program pandagma pan, version 2023-02-29 Run started at: Wed Nov 27 20:04:05 CST 2024 Run ended at: Sat Nov 30 11:16:59 CST 2024 Sequence type: nucleotide Parameter value clust_iden 0.90 clust_cov 0.50 clust_cov_extra 0.40 extra_iden 0.70 mcl_inflation 1.6 strict_synt 1 pctl_low 25 pctl_med 50 pctl_hi 75 consen_prefix Zea.pan3 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 73016 largest_cluster 112 modal_clst_size 2 num_at_mode 17659 seqs_clustered 933609 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 80770 largest_cluster 142 modal_clst_size 2 num_at_mode 21703 seqs_clustered 971106 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl25 set consists of orthogroups with at least 15 genes per OG (>= 57 * 25/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 80770 largest_cluster 486 modal_clst_size>=15 57 num_at_mode>=15 5512 seqs_clustered 2106263 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 39756 153 16278 1452 1102.1 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- Extra: 37828 84 25046 1968 1619.9 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: 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: 42423 90 16392 1465 1108 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 37796 5 16278 1497 1173.9 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 37828 34541 30643 91.3 81.0 5b+ 49202 34016 29683 69.1 60.3 Zm00001d 39756 35615 30475 89.6 76.7 Zm00001eb 40690 38461 33440 94.5 82.2 Zm00004b 40557 35075 30824 86.5 76.0 Zm00008a 46105 37351 33640 81.0 73.0 Zm00010a 48370 37603 33797 77.7 69.9 Zm00011a 42580 36862 32366 86.6 76.0 Zm00014ba 43271 37636 32457 87.0 75.0 Zm00015a 48140 38979 34212 81.0 71.1 Zm00016a 48306 39307 34536 81.4 71.5 Zm00017a 40368 36493 30774 90.4 76.2 Zm00018ab 40473 34592 30067 85.5 74.3 Zm00019ab 40272 35475 30311 88.1 75.3 Zm00020ab 40013 35879 30655 89.7 76.6 Zm00021ab 41577 35777 30537 86.0 73.4 Zm00022ab 40383 36041 30679 89.2 76.0 Zm00023ab 40325 35808 30560 88.8 75.8 Zm00024ab 41122 36100 30780 87.8 74.9 Zm00025ab 40428 35855 30704 88.7 75.9 Zm00026ab 39785 35797 30631 90.0 77.0 Zm00027ab 40290 35877 30529 89.0 75.8 Zm00028ab 41059 36245 30889 88.3 75.2 Zm00029ab 39868 35892 30749 90.0 77.1 Zm00030ab 40778 36620 31002 89.8 76.0 Zm00031ab 40905 36441 30965 89.1 75.7 Zm00032ab 41486 36365 30858 87.7 74.4 Zm00033ab 41204 36380 30859 88.3 74.9 Zm00034ab 41247 36412 30819 88.3 74.7 Zm00035ab 40484 36188 30808 89.4 76.1 Zm00036ab 39787 36104 30835 90.7 77.5 Zm00037ab 40334 36254 30778 89.9 76.3 Zm00038ab 39973 36099 30828 90.3 77.1 Zm00039ab 41478 36137 30551 87.1 73.7 Zm00040ab 41164 36470 30957 88.6 75.2 Zm00041ab 41593 36174 30710 87.0 73.8 Zm00042ab 38368 33322 28408 86.8 74.0 Zm00045a 38238 33813 28882 88.4 75.5 Zm00054a 40747 36566 32309 89.7 79.3 Zm00056aa 45287 39340 35396 86.9 78.2 Zm00092aa 42500 36935 33688 86.9 79.3 Zm00093aa 43718 37274 33669 85.3 77.0 Zm00094aa 44771 38545 34930 86.1 78.0 Zm00095aa 46311 39444 35326 85.2 76.3 Zm00096aa 45537 39428 35656 86.6 78.3 Zm00097aa 45809 39378 35345 86.0 77.2 Zm00099aa 44719 38289 34367 85.6 76.9 Zm00100aa 44191 37951 34111 85.9 77.2 Zm00101aa 44791 38503 34710 86.0 77.5 Zm00102aa 44845 38699 35028 86.3 78.1 Zm00103aa 40104 35597 30250 88.8 75.4 Zm00106aa 39298 36614 32443 93.2 82.6 Zm00107aa 42075 37111 33034 88.2 78.5 Zm00108aa 40357 36863 32183 91.3 79.7 Zm00109aa 44482 40455 34165 90.9 76.8 Zm00110aa 48487 41972 34558 86.6 71.3 Zm00111aa 52317 43243 35715 82.7 68.3 Zm00112aa == 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 34541 31409 90.93 38.89 61.11 5b+ 34016 32656 96.00 40.43 59.57 Zm00001d 35615 34626 97.22 42.87 57.13 Zm00001eb 38461 34430 89.52 42.63 57.37 Zm00004b 35075 32135 91.62 39.79 60.21 Zm00008a 37351 34520 92.42 42.74 57.26 Zm00010a 37603 34680 92.23 42.94 57.06 Zm00011a 36862 34065 92.41 42.18 57.82 Zm00014ba 37636 34311 91.17 42.48 57.52 Zm00015a 38979 34995 89.78 43.33 56.67 Zm00016a 39307 35295 89.79 43.70 56.30 Zm00017a 36493 35562 97.45 44.03 55.97 Zm00018ab 34592 33624 97.20 41.63 58.37 Zm00019ab 35475 34546 97.38 42.77 57.23 Zm00020ab 35879 34957 97.43 43.28 56.72 Zm00021ab 35777 34832 97.36 43.12 56.88 Zm00022ab 36041 35149 97.53 43.52 56.48 Zm00023ab 35808 34908 97.49 43.22 56.78 Zm00024ab 36100 35134 97.32 43.50 56.50 Zm00025ab 35855 34921 97.40 43.24 56.76 Zm00026ab 35797 34901 97.50 43.21 56.79 Zm00027ab 35877 34932 97.37 43.25 56.75 Zm00028ab 36245 35313 97.43 43.72 56.28 Zm00029ab 35892 34967 97.42 43.29 56.71 Zm00030ab 36620 35700 97.49 44.20 55.80 Zm00031ab 36441 35461 97.31 43.90 56.10 Zm00032ab 36365 35356 97.23 43.77 56.23 Zm00033ab 36380 35454 97.45 43.90 56.10 Zm00034ab 36412 35441 97.33 43.88 56.12 Zm00035ab 36188 35212 97.30 43.60 56.40 Zm00036ab 36104 35185 97.45 43.56 56.44 Zm00037ab 36254 35365 97.55 43.78 56.22 Zm00038ab 36099 35224 97.58 43.61 56.39 Zm00039ab 36137 35127 97.21 43.49 56.51 Zm00040ab 36470 35489 97.31 43.94 56.06 Zm00041ab 36174 35228 97.38 43.62 56.38 Zm00042ab 33322 29789 89.40 36.88 63.12 Zm00045a 33813 30574 90.42 37.85 62.15 Zm00054a 36566 33026 90.32 40.89 59.11 Zm00056aa 39340 35568 90.41 44.04 55.96 Zm00092aa 36935 33718 91.29 41.75 58.25 Zm00093aa 37274 33986 91.18 42.08 57.92 Zm00094aa 38545 34874 90.48 43.18 56.82 Zm00095aa 39444 35714 90.54 44.22 55.78 Zm00096aa 39428 35636 90.38 44.12 55.88 Zm00097aa 39378 35677 90.60 44.17 55.83 Zm00099aa 38289 34629 90.44 42.87 57.13 Zm00100aa 37951 34465 90.81 42.67 57.33 Zm00101aa 38503 35043 91.01 43.39 56.61 Zm00102aa 38699 35237 91.05 43.63 56.37 Zm00103aa 35597 31718 89.10 39.27 60.73 Zm00106aa 36614 33388 91.19 41.34 58.66 Zm00107aa 37111 33336 89.83 41.27 58.73 Zm00108aa 36863 32657 88.59 40.43 59.57 Zm00109aa 40455 35796 88.48 44.32 55.68 Zm00110aa 41972 34833 82.99 43.13 56.87 Zm00111aa 43243 35805 82.80 44.33 55.67 Zm00112aa Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 1 1 2 17659 3 8365 4 4806 5 3239 6 2380 7 1784 8 1401 9 1105 10 860 11 803 12 695 13 590 14 541 15 504 16 457 17 416 18 428 19 446 20 429 21 453 22 529 23 608 24 875 25 1513 26 4157 27 15723 28 833 29 298 30 163 31 123 32 94 33 59 34 56 35 63 36 47 37 48 38 41 39 34 40 26 41 39 42 26 43 28 44 25 45 18 46 12 47 21 48 16 49 19 50 21 51 17 52 16 53 20 54 5 55 6 56 3 57 10 58 3 59 5 60 7 61 6 62 3 63 4 64 3 65 2 66 3 68 4 69 1 70 1 71 1 72 1 73 1 74 2 76 4 77 1 78 2 79 1 81 2 85 1 88 1 95 1 112 2 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 1 1 2 21703 3 9669 4 5474 5 3608 6 2611 7 1942 8 1499 9 1174 10 916 11 855 12 757 13 635 14 575 15 542 16 487 17 442 18 455 19 471 20 461 21 477 22 557 23 638 24 901 25 1566 26 4201 27 15853 28 839 29 300 30 164 31 123 32 98 33 61 34 59 35 64 36 47 37 51 38 41 39 35 40 27 41 39 42 26 43 29 44 28 45 19 46 13 47 22 48 17 49 19 50 21 51 18 52 17 53 20 54 6 55 6 56 4 57 11 58 3 59 5 60 8 61 6 62 3 63 4 64 4 65 2 66 3 68 5 69 1 70 1 71 1 72 1 73 2 74 3 76 5 77 1 78 2 79 2 81 3 85 1 86 1 88 1 93 1 95 1 103 1 109 1 112 2 124 1 142 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 1 1 2 7330 3 5887 4 4738 5 3871 6 3297 7 2872 8 2554 9 2192 10 1899 11 1660 12 1569 13 1370 14 1194 15 1140 16 987 17 944 18 871 19 772 20 680 21 656 22 612 23 562 24 506 25 507 26 451 27 403 28 370 29 329 30 313 31 347 32 297 33 277 34 296 35 267 36 252 37 249 38 241 39 230 40 229 41 235 42 234 43 262 44 234 45 267 46 301 47 304 48 366 49 374 50 475 51 568 52 810 53 1169 54 1895 55 3376 56 5341 57 5512 58 2053 59 845 60 511 61 335 62 268 63 193 64 168 65 120 66 102 67 105 68 74 69 79 70 67 71 54 72 51 73 42 74 37 75 31 76 27 77 21 78 21 79 26 80 24 81 19 82 21 83 19 84 21 85 12 86 7 87 16 88 10 89 12 90 15 91 14 92 9 93 10 94 10 95 13 96 15 97 10 98 12 99 10 100 9 101 15 102 9 103 18 104 7 105 14 106 12 107 6 108 11 109 9 110 11 111 13 112 13 113 7 114 6 115 5 116 9 117 6 118 3 119 2 120 2 121 4 122 4 123 4 124 3 125 2 126 3 127 1 128 4 129 2 130 4 131 3 132 3 133 1 134 3 135 2 136 1 137 6 138 1 139 1 140 1 141 1 142 2 143 1 145 3 146 3 148 1 149 2 151 2 152 1 153 1 154 2 155 1 156 3 157 2 158 1 160 2 161 1 162 1 163 2 166 1 171 1 172 1 173 2 174 1 176 1 179 1 180 2 181 1 182 1 183 1 184 1 185 1 189 1 193 1 195 1 198 4 202 1 208 2 210 2 211 1 213 1 220 1 227 1 234 1 236 1 240 1 244 1 257 1 270 1 282 2 286 1 289 1 349 1 461 1 486 1