Run of program pandagma pan, version 2023-01-28 Run started at: Wed Jan 31 08:25:12 PM CST 2024 Run ended at: Wed Jan 31 09:30:35 PM CST 2024 Sequence type: nucleotide Parameter value clust_iden 0.95 clust_cov 0.50 extra_iden 0.75 mcl_inflation 1.6 strict_synt 1 pctl_low 30 pctl_med 50 pctl_hi 75 consen_prefix Arachis.pan2 annot_str_regex ([^.]+\.[^.]+\.[^.]+\.[^.]+)\..+ order_method reference preferred_annot Tifrunner.gnm2.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 72151 largest_cluster 10 modal_clst_size 3 num_at_mode 22824 seqs_clustered 239146 == Augmented clusters (unanchored sequences added to the initial clusters) Cluster file 12_syn_pan_aug.clust.tsv num_of_clusters 87287 largest_cluster 55 modal_clst_size 2 num_at_mode 29538 seqs_clustered 286263 == Augmented-extra clusters (with sequences from extra annotation sets) The pctl30 set consists of orthogroups with at least 3 genes per OG (>= 7 * 30/100 sets). Cluster file 18_syn_pan_aug_extra.clust.tsv num_of_clusters 87287 largest_cluster 68 modal_clst_size>=3 3 num_at_mode>=3 20215 seqs_clustered 367063 == Sequence stats for CDS files Class: seqs min max N50 ave annotation_name Main: 62236 15 16272 1566 1187.5 arahy.BaileyII.gnm1.ann1 Main: 66939 75 16374 1584 1189.1 arahy.Tifrunner.gnm1.ann1 Main: 63951 90 16272 1575 1289.3 arahy.Tifrunner.gnm1.ann2 Main: 66821 75 16374 1581 1186.9 arahy.Tifrunner.gnm2.ann1 Main: 82883 78 16272 1479 1087.3 arahy.Tifrunner.gnm2.ann2 Extra: 78133 75 19380 1488 1075.3 araduip.V14167K30076.gnm1.ann1 Extra: 32033 111 16272 1605 1325.6 arast.V10309.gnm1.ann1 Avg: 64713 74 16745 1554 1191 all_annot_sets == Sequence stats for final pangene CDS files -- pctl30 and trimmed Class: seqs min max N50 ave annotation_name pctl30: 68952 78 16374 1599 1243.7 23_syn_pan_pctl30_posn_cds.fna == Proportion of initial genes retained in the "aug_extra" and "pctl30" sets: Start End_all End_core Pct_kept_all Pct_kept_core Annotation_name 78133 56167 55622 71.9 71.2 araduip.V14167K30076.gnm1.ann1 62236 47090 41398 75.7 66.5 arahy.BaileyII.gnm1.ann1 66939 62509 53114 93.4 79.3 arahy.Tifrunner.gnm1.ann1 63951 48658 44577 76.1 69.7 arahy.Tifrunner.gnm1.ann2 66821 61153 52227 91.5 78.2 arahy.Tifrunner.gnm2.ann1 82883 66853 59521 80.7 71.8 arahy.Tifrunner.gnm2.ann2 32033 24633 24543 76.9 76.6 arast.V10309.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 56167 50356 89.65 57.69 42.31 araduip.V14167K30076.gnm1.ann1 47090 46568 98.89 53.35 46.65 arahy.BaileyII.gnm1.ann1 62509 61877 98.99 70.89 29.11 arahy.Tifrunner.gnm1.ann1 48658 47790 98.22 54.75 45.25 arahy.Tifrunner.gnm1.ann2 61153 60546 99.01 69.36 30.64 arahy.Tifrunner.gnm2.ann1 66853 65445 97.89 74.98 25.02 arahy.Tifrunner.gnm2.ann2 24633 22976 93.27 26.32 73.68 arast.V10309.gnm1.ann1 Counts of initial clusters by cluster size, file 06_syn_pan.clust.tsv: 2 22554 3 22824 4 9006 5 17308 6 263 7 156 8 31 9 6 10 3 Counts of augmented clusters by cluster size, file 12_syn_pan_aug.clust.tsv: 2 29538 3 26805 4 9857 5 20273 6 392 7 224 8 77 9 38 10 36 11 13 12 6 13 9 14 3 15 1 17 3 18 3 19 2 20 1 23 2 27 1 28 1 33 1 55 1 Counts of augmented-extra clusters by cluster size, file 18_syn_pan_aug_extra.clust.tsv: 2 17072 3 20215 4 15330 5 10441 6 14165 7 8753 8 716 9 243 10 117 11 63 12 59 13 33 14 15 15 15 16 11 17 7 18 6 19 1 20 4 21 3 22 1 23 3 24 3 25 1 27 2 28 1 32 1 33 1 35 2 38 1 62 1 68 1