Run of program pandagma pan, version 2023-02-23 Run started at: Sun 25 Feb 2024 06:19:07 AM PST Run ended at: Mon 26 Feb 2024 07:16:43 AM PST 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 Glycine.pan5 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method alignment preferred_annot Wm82.gnm6.ann1 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 88105 largest_cluster 66 modal_clst_size 21 num_at_mode 20554 seqs_clustered 1055955 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 93298 largest_cluster 115 modal_clst_size 21 num_at_mode 20724 seqs_clustered 1088709 == 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 93298 largest_cluster 530 modal_clst_size>=15 57 num_at_mode>=15 4831 seqs_clustered 2954022 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 52345 87 16383 1578 1195.6 glyma.FiskebyIII.gnm1.ann1 Main: 57824 150 15024 1494 1102.8 glyma.Hefeng25_IGA1002.gnm1.ann1 Main: 57049 150 17403 1518 1116.7 glyma.Huaxia3_IGA1007.gnm1.ann1 Main: 52734 150 16308 1518 1168.1 glyma.JD17.gnm1.ann1 Main: 58090 150 15078 1488 1099.3 glyma.Jinyuan_IGA1006.gnm1.ann1 Main: 47576 90 16383 1593 1237.8 glyma.Lee.gnm1.ann1 Main: 51755 150 16290 1542 1175.4 glyma.Lee.gnm2.ann1 Main: 56462 149 16521 1491 1116.3 glyma.Lee.gnm3.ann1 Main: 57224 150 16338 1512 1119.2 glyma.Wenfeng7_IGA1001.gnm1.ann1 Main: 55832 87 16308 1569 1169.7 glyma.Wm82.gnm2.ann1 Main: 52816 90 16308 1572 1156.2 glyma.Wm82.gnm4.ann1 Main: 58105 150 16359 1476 1095.9 glyma.Wm82.gnm5.ann1 Main: 48310 63 16308 1602 1238.8 glyma.Wm82.gnm6.ann1 Main: 56786 150 16338 1521 1125.3 glyma.Wm82_IGA1008.gnm1.ann1 Main: 55217 90 16308 1554 1142.5 glyma.Wm82_NJAU.gnm1.ann1 Main: 57175 150 16338 1506 1110.4 glyma.Zh13_IGA1005.gnm1.ann1 Main: 51846 90 16308 1605 1270.5 glyma.Zh13.gnm1.ann1 Main: 57876 150 14778 1503 1112.5 glyma.Zh35_IGA1004.gnm1.ann1 Main: 57658 150 15993 1500 1104.0 glyso.F_IGA1003.gnm1.ann1 Main: 46904 90 15327 1581 1238.8 glyso.PI483463.gnm1.ann1 Main: 55188 150 15867 1578 1204.6 glyso.W05.gnm1.ann1 Extra: 58619 90 15327 1485 1087.8 glyma.58-161.gnm1.ann1 Extra: 57770 90 16248 1494 1091.8 glyma.Amsoy.gnm1.ann1 Extra: 54788 90 26136 1533 1117.1 glyma.DongNongNo_50.gnm1.ann1 Extra: 58022 90 16281 1497 1095.4 glyma.FengDiHuang.gnm1.ann1 Extra: 55690 90 23778 1599 1159.6 glyma.HanDouNo_5.gnm1.ann1 Extra: 57741 90 15696 1473 1074.8 glyma.HeiHeNo_43.gnm1.ann1 Extra: 53173 162 18807 1668 1300.5 glyma.Hwangkeum.gnm1.ann1 Extra: 56494 90 23502 1599 1160.9 glyma.JiDouNo_17.gnm1.ann1 Extra: 54543 90 19887 1530 1117.7 glyma.JinDouNo_23.gnm1.ann1 Extra: 57550 90 16305 1488 1090.0 glyma.JuXuanNo_23.gnm1.ann1 Extra: 55043 90 27738 1545 1125.9 glyma.KeShanNo_1.gnm1.ann1 Extra: 55855 90 24426 1542 1124.3 glyma.PI_398296.gnm1.ann1 Extra: 55755 90 17376 1593 1156.9 glyma.PI_548362.gnm1.ann1 Extra: 54509 90 21267 1527 1113.9 glyma.QiHuangNo_34.gnm1.ann1 Extra: 59346 90 16281 1509 1104.0 glyma.ShiShengChangYe.gnm1.ann1 Extra: 54951 90 31023 1557 1132.1 glyma.TieFengNo_18.gnm1.ann1 Extra: 58244 93 16170 1509 1101.2 glyma.TieJiaSiLiHuang.gnm1.ann1 Extra: 55541 90 21525 1545 1127.3 glyma.TongShanTianEDan.gnm1.ann1 Extra: 57562 90 16281 1491 1094.7 glyma.WanDouNo_28.gnm1.ann1 Extra: 54041 72 58035 1575 1186.6 glyma.Wm82.gnm1.ann1 Extra: 48310 63 16308 1602 1238.8 glyma.Wm82_ISU01.gnm2.ann1 Extra: 54184 90 21840 1518 1106.9 glyma.XuDouNo_1.gnm1.ann1 Extra: 55379 90 23409 1575 1143.6 glyma.YuDouNo_22.gnm1.ann1 Extra: 55328 77 17961 2375 1722.4 glyma.Zh13.gnm2.ann1 Extra: 56312 90 23529 1575 1141.2 glyma.ZhangChunManCangJin.gnm1.ann1 Extra: 54270 90 17163 1524 1108.8 glyma.Zhutwinning2.gnm1.ann1 Extra: 54576 90 18180 1539 1120.6 glyma.ZiHuaNo_4.gnm1.ann1 Extra: 55296 90 16779 1599 1162.0 glyso.PI_549046.gnm1.ann1 Extra: 57692 90 16305 1515 1110.8 glyso.PI_562565.gnm1.ann1 Extra: 57613 90 16251 1467 1075.5 glyso.PI_578357.gnm1.ann1 Extra: 55325 90 19512 1413 1026.0 glycy.G1267.gnm1.ann1 Extra: 55739 90 14457 1401 1021.8 glyd3.G1403.gnm1.ann1 Extra: 111663 90 15420 1251 902.9 glydo.G1134.gnm1.ann1 Extra: 56634 90 17001 1410 1019.9 glyfa.G1718.gnm1.ann1 Extra: 55472 90 15702 1374 1014.2 glyst.G1974.gnm1.ann1 Extra: 54347 90 18831 1419 1036.9 glysy.G1300.gnm1.ann1 Avg: 56283 103 18754 1537 1137 all_annot_sets == Sequence stats for final pangene CDS files -- pctl25 and trimmed Class: seqs min max N50 ave annotation_name pctl25: 57686 102 16236 1542 1156.5 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 55325 46005 42131 83.2 76.2 glycy.G1267.gnm1.ann1 55739 45900 42025 82.3 75.4 glyd3.G1403.gnm1.ann1 111663 86931 78637 77.9 70.4 glydo.G1134.gnm1.ann1 56634 46895 42583 82.8 75.2 glyfa.G1718.gnm1.ann1 58619 54168 52605 92.4 89.7 glyma.58-161.gnm1.ann1 57770 54012 52796 93.5 91.4 glyma.Amsoy.gnm1.ann1 54788 50325 49060 91.9 89.5 glyma.DongNongNo_50.gnm1.ann1 58022 54233 53113 93.5 91.5 glyma.FengDiHuang.gnm1.ann1 52345 48574 44986 92.8 85.9 glyma.FiskebyIII.gnm1.ann1 55690 51886 50887 93.2 91.4 glyma.HanDouNo_5.gnm1.ann1 57824 55765 45124 96.4 78.0 glyma.Hefeng25_IGA1002.gnm1.ann1 57741 53465 52147 92.6 90.3 glyma.HeiHeNo_43.gnm1.ann1 57049 55078 45589 96.5 79.9 glyma.Huaxia3_IGA1007.gnm1.ann1 53173 46413 42574 87.3 80.1 glyma.Hwangkeum.gnm1.ann1 52734 49434 45166 93.7 85.6 glyma.JD17.gnm1.ann1 56494 52370 51409 92.7 91.0 glyma.JiDouNo_17.gnm1.ann1 54543 50512 49409 92.6 90.6 glyma.JinDouNo_23.gnm1.ann1 58090 55600 44783 95.7 77.1 glyma.Jinyuan_IGA1006.gnm1.ann1 57550 53681 52445 93.3 91.1 glyma.JuXuanNo_23.gnm1.ann1 55043 50859 49849 92.4 90.6 glyma.KeShanNo_1.gnm1.ann1 47576 46698 43893 98.2 92.3 glyma.Lee.gnm1.ann1 51755 48328 43907 93.4 84.8 glyma.Lee.gnm2.ann1 56462 53047 44338 94.0 78.5 glyma.Lee.gnm3.ann1 55855 50874 49738 91.1 89.0 glyma.PI_398296.gnm1.ann1 55755 52032 51140 93.3 91.7 glyma.PI_548362.gnm1.ann1 54509 50411 49276 92.5 90.4 glyma.QiHuangNo_34.gnm1.ann1 59346 54390 53260 91.6 89.7 glyma.ShiShengChangYe.gnm1.ann1 54951 50956 49912 92.7 90.8 glyma.TieFengNo_18.gnm1.ann1 58244 54606 53373 93.8 91.6 glyma.TieJiaSiLiHuang.gnm1.ann1 55541 50919 49802 91.7 89.7 glyma.TongShanTianEDan.gnm1.ann1 57562 53740 52407 93.4 91.0 glyma.WanDouNo_28.gnm1.ann1 57224 55086 45709 96.3 79.9 glyma.Wenfeng7_IGA1001.gnm1.ann1 54041 51906 47619 96.0 88.1 glyma.Wm82.gnm1.ann1 55832 53366 47339 95.6 84.8 glyma.Wm82.gnm2.ann1 52816 52231 45902 98.9 86.9 glyma.Wm82.gnm4.ann1 58105 54118 45244 93.1 77.9 glyma.Wm82.gnm5.ann1 48310 47271 44542 97.8 92.2 glyma.Wm82.gnm6.ann1 56786 55097 46615 97.0 82.1 glyma.Wm82_IGA1008.gnm1.ann1 48310 47769 45297 98.9 93.8 glyma.Wm82_ISU01.gnm2.ann1 55217 53269 46632 96.5 84.5 glyma.Wm82_NJAU.gnm1.ann1 54184 50047 48761 92.4 90.0 glyma.XuDouNo_1.gnm1.ann1 55379 51395 50354 92.8 90.9 glyma.YuDouNo_22.gnm1.ann1 51846 47737 44403 92.1 85.6 glyma.Zh13.gnm1.ann1 55328 45966 44082 83.1 79.7 glyma.Zh13.gnm2.ann1 57175 55364 45519 96.8 79.6 glyma.Zh13_IGA1005.gnm1.ann1 57876 55264 45767 95.5 79.1 glyma.Zh35_IGA1004.gnm1.ann1 56312 52093 50823 92.5 90.3 glyma.ZhangChunManCangJin.gnm1.ann1 54270 49998 48704 92.1 89.7 glyma.Zhutwinning2.gnm1.ann1 54576 50413 49124 92.4 90.0 glyma.ZiHuaNo_4.gnm1.ann1 57658 51524 44569 89.4 77.3 glyso.F_IGA1003.gnm1.ann1 46904 45413 42643 96.8 90.9 glyso.PI483463.gnm1.ann1 55296 51377 49926 92.9 90.3 glyso.PI_549046.gnm1.ann1 57692 54050 52304 93.7 90.7 glyso.PI_562565.gnm1.ann1 57613 52842 50969 91.7 88.5 glyso.PI_578357.gnm1.ann1 55188 50445 45721 91.4 82.8 glyso.W05.gnm1.ann1 55472 46584 42633 84.0 76.9 glyst.G1974.gnm1.ann1 54347 45290 41675 83.3 76.7 glysy.G1300.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 46005 38468 83.62 41.23 58.77 glycy.G1267.gnm1.ann1 45900 37357 81.39 40.04 59.96 glyd3.G1403.gnm1.ann1 86931 45376 52.20 48.64 51.36 glydo.G1134.gnm1.ann1 46895 38148 81.35 40.89 59.11 glyfa.G1718.gnm1.ann1 54168 52621 97.14 56.40 43.60 glyma.58-161.gnm1.ann1 54012 52523 97.24 56.30 43.70 glyma.Amsoy.gnm1.ann1 50325 49107 97.58 52.63 47.37 glyma.DongNongNo_50.gnm1.ann1 54233 52757 97.28 56.55 43.45 glyma.FengDiHuang.gnm1.ann1 48574 47976 98.77 51.42 48.58 glyma.FiskebyIII.gnm1.ann1 51886 50631 97.58 54.27 45.73 glyma.HanDouNo_5.gnm1.ann1 55765 55327 99.21 59.30 40.70 glyma.Hefeng25_IGA1002.gnm1.ann1 53465 52019 97.30 55.76 44.24 glyma.HeiHeNo_43.gnm1.ann1 55078 54692 99.30 58.62 41.38 glyma.Huaxia3_IGA1007.gnm1.ann1 46413 44675 96.26 47.88 52.12 glyma.Hwangkeum.gnm1.ann1 49434 49035 99.19 52.56 47.44 glyma.JD17.gnm1.ann1 52370 50792 96.99 54.44 45.56 glyma.JiDouNo_17.gnm1.ann1 50512 49321 97.64 52.86 47.14 glyma.JinDouNo_23.gnm1.ann1 55600 55200 99.28 59.17 40.83 glyma.Jinyuan_IGA1006.gnm1.ann1 53681 52285 97.40 56.04 43.96 glyma.JuXuanNo_23.gnm1.ann1 50859 49647 97.62 53.21 46.79 glyma.KeShanNo_1.gnm1.ann1 46698 46309 99.17 49.64 50.36 glyma.Lee.gnm1.ann1 48328 48162 99.66 51.62 48.38 glyma.Lee.gnm2.ann1 53047 52494 98.96 56.26 43.74 glyma.Lee.gnm3.ann1 50874 49642 97.58 53.21 46.79 glyma.PI_398296.gnm1.ann1 52032 50777 97.59 54.42 45.58 glyma.PI_548362.gnm1.ann1 50411 49226 97.65 52.76 47.24 glyma.QiHuangNo_34.gnm1.ann1 54390 52875 97.21 56.67 43.33 glyma.ShiShengChangYe.gnm1.ann1 50956 49785 97.70 53.36 46.64 glyma.TieFengNo_18.gnm1.ann1 54606 53121 97.28 56.94 43.06 glyma.TieJiaSiLiHuang.gnm1.ann1 50919 49600 97.41 53.16 46.84 glyma.TongShanTianEDan.gnm1.ann1 53740 52287 97.30 56.04 43.96 glyma.WanDouNo_28.gnm1.ann1 55086 54670 99.24 58.60 41.40 glyma.Wenfeng7_IGA1001.gnm1.ann1 51906 50962 98.18 54.62 45.38 glyma.Wm82.gnm1.ann1 53366 52884 99.10 56.68 43.32 glyma.Wm82.gnm2.ann1 52231 51862 99.29 55.59 44.41 glyma.Wm82.gnm4.ann1 54118 53426 98.72 57.26 42.74 glyma.Wm82.gnm5.ann1 47271 46862 99.13 50.23 49.77 glyma.Wm82.gnm6.ann1 55097 54710 99.30 58.64 41.36 glyma.Wm82_IGA1008.gnm1.ann1 47769 47191 98.79 50.58 49.42 glyma.Wm82_ISU01.gnm2.ann1 53269 52890 99.29 56.69 43.31 glyma.Wm82_NJAU.gnm1.ann1 50047 48863 97.63 52.37 47.63 glyma.XuDouNo_1.gnm1.ann1 51395 50174 97.62 53.78 46.22 glyma.YuDouNo_22.gnm1.ann1 47737 47314 99.11 50.71 49.29 glyma.Zh13.gnm1.ann1 45966 43433 94.49 46.55 53.45 glyma.Zh13.gnm2.ann1 55364 55021 99.38 58.97 41.03 glyma.Zh13_IGA1005.gnm1.ann1 55264 54711 99.00 58.64 41.36 glyma.Zh35_IGA1004.gnm1.ann1 52093 50525 96.99 54.15 45.85 glyma.ZhangChunManCangJin.gnm1.ann1 49998 48797 97.60 52.30 47.70 glyma.Zhutwinning2.gnm1.ann1 50413 49254 97.70 52.79 47.21 glyma.ZiHuaNo_4.gnm1.ann1 51524 51179 99.33 54.86 45.14 glyso.F_IGA1003.gnm1.ann1 45413 45054 99.21 48.29 51.71 glyso.PI483463.gnm1.ann1 51377 50168 97.65 53.77 46.23 glyso.PI_549046.gnm1.ann1 54050 52508 97.15 56.28 43.72 glyso.PI_562565.gnm1.ann1 52842 51292 97.07 54.98 45.02 glyso.PI_578357.gnm1.ann1 50445 49961 99.04 53.55 46.45 glyso.W05.gnm1.ann1 46584 38784 83.26 41.57 58.43 glyst.G1974.gnm1.ann1 45290 37293 82.34 39.97 60.03 glysy.G1300.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 14054 3 7152 4 4620 5 3409 6 2986 7 2833 8 2570 9 2010 10 2026 11 1800 12 1641 13 1643 14 1472 15 1521 16 1691 17 1969 18 2654 19 4064 20 6769 21 20554 22 332 23 43 24 31 25 27 26 24 27 20 28 17 29 15 30 24 31 17 32 11 33 9 34 12 35 16 36 13 37 12 38 8 39 8 40 12 41 4 42 2 43 2 45 1 46 1 48 3 53 1 57 1 66 1 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 16057 3 7917 4 5040 5 3672 6 3177 7 2996 8 2717 9 2127 10 2119 11 1906 12 1731 13 1757 14 1555 15 1593 16 1765 17 2032 18 2724 19 4142 20 6820 21 20724 22 340 23 46 24 33 25 32 26 25 27 23 28 18 29 15 30 27 31 21 32 16 33 9 34 13 35 16 36 13 37 13 38 8 39 9 40 13 41 7 42 3 43 2 45 1 46 2 48 3 51 1 53 2 54 1 55 1 56 2 57 1 58 1 59 1 66 2 75 1 83 1 85 1 96 1 97 1 108 1 115 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 6688 3 4900 4 4034 5 3188 6 2889 7 2441 8 2297 9 1922 10 1667 11 1348 12 1229 13 1068 14 855 15 846 16 787 17 725 18 666 19 569 20 542 21 522 22 504 23 523 24 513 25 540 26 549 27 608 28 646 29 760 30 732 31 729 32 684 33 706 34 734 35 732 36 725 37 705 38 718 39 749 40 799 41 773 42 720 43 790 44 733 45 740 46 820 47 841 48 987 49 1144 50 1445 51 1604 52 1929 53 2274 54 2811 55 3356 56 4154 57 4831 58 4437 59 2124 60 1306 61 846 62 628 63 529 64 358 65 261 66 169 67 103 68 91 69 53 70 53 71 40 72 34 73 29 74 33 75 20 76 15 77 25 78 19 79 25 80 19 81 19 82 14 83 18 84 12 85 20 86 16 87 9 88 6 89 5 90 8 91 8 92 9 93 6 94 8 95 6 96 5 97 6 98 4 99 4 100 3 101 5 102 4 103 2 104 3 105 6 106 3 107 5 108 1 109 1 110 3 111 2 112 3 113 5 114 3 115 4 118 1 119 3 120 1 121 1 123 1 124 1 125 2 126 2 127 1 131 1 132 2 133 1 136 1 137 2 138 1 142 1 143 1 144 2 145 1 148 1 150 2 156 1 162 1 164 1 165 2 167 1 169 2 181 1 183 1 187 1 188 1 193 1 219 1 238 1 257 1 262 1 268 1 278 1 304 1 318 1 327 2 485 1 530 1