## The number of loci caught by each filter. ## ipyrad API location: [assembly].stats_dfs.s7_filters total_filters applied_order retained_loci total_prefiltered_loci 0 0 16914 filtered_by_rm_duplicates 283 283 16631 filtered_by_max_indels 822 822 15809 filtered_by_max_SNPs 2 0 15809 filtered_by_max_shared_het 672 617 15192 filtered_by_min_sample 6881 6881 8311 total_filtered_loci 8660 8603 8311 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage Paguio-CB5 5285 Paguio-DB11 5515 Paguio-DB13 842 Paguio-DB22 1493 Paguio-DB23 4687 Paguio-DB8 48 Paguio-DE12 3 Paguio-DE21 1 Paguio-DE23 94 Paguio-DE7 11 Paguio-G88 2244 Paguio-KB103 2105 Paguio-KB106 1328 Paguio-KB108 6003 Paguio-KB79 3974 Paguio-MB74 5919 Paguio-MB77 6302 Paguio-MB83 5429 Paguio-MB88 8 Paguio-NS24 5435 Paguio-NS9 6356 Paguio-RB20 5241 Paguio-RB35 3831 Paguio-RB36 1250 ## The number of loci for which N taxa have data. ## ipyrad API location: [assembly].stats_dfs.s7_loci locus_coverage sum_coverage 1 0 0 2 0 0 3 0 0 4 1308 1308 5 935 2243 6 820 3063 7 708 3771 8 668 4439 9 585 5024 10 548 5572 11 521 6093 12 496 6589 13 439 7028 14 387 7415 15 280 7695 16 235 7930 17 161 8091 18 163 8254 19 50 8304 20 5 8309 21 1 8310 22 1 8311 23 0 8311 24 0 8311 The distribution of SNPs (var and pis) per locus. ## var = Number of loci with n variable sites (pis + autapomorphies) ## pis = Number of loci with n parsimony informative site (minor allele in >1 sample) ## ipyrad API location: [assembly].stats_dfs.s7_snps ## The "reference" sample is included if present unless 'exclude_reference=True' var sum_var pis sum_pis 0 3430 0 4833 0 1 1824 1824 1503 1503 2 1047 3918 770 3043 3 617 5769 425 4318 4 395 7349 248 5310 5 254 8619 162 6120 6 181 9705 113 6798 7 118 10531 52 7162 8 77 11147 50 7562 9 67 11750 46 7976 10 55 12300 32 8296 11 30 12630 11 8417 12 36 13062 17 8621 13 19 13309 10 8751 14 35 13799 13 8933 15 21 14114 7 9038 16 16 14370 5 9118 17 12 14574 2 9152 18 8 14718 0 9152 19 10 14908 2 9190 20 7 15048 2 9230 21 7 15195 0 9230 22 4 15283 2 9274 23 7 15444 2 9320 24 4 15540 0 9320 25 2 15590 0 9320 26 3 15668 2 9372 27 4 15776 0 9372 28 5 15916 1 9400 29 2 15974 0 9400 30 1 16004 0 9400 31 1 16035 0 9400 32 1 16067 0 9400 33 2 16133 1 9433 34 2 16201 0 9433 35 0 16201 0 9433 36 2 16273 0 9433 37 1 16310 0 9433 38 0 16310 0 9433 39 1 16349 0 9433 40 1 16389 0 9433 41 2 16471 0 9433 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly Paguio-CB5 7 712885 705578 21368 7767 0.009412 0.001457 6898 5285 Paguio-DB11 7 1041179 1033204 23182 8389 0.009871 0.001393 7396 5515 Paguio-DB13 7 79407 78701 7891 1457 0.016572 0.003920 1137 842 Paguio-DB22 7 175128 173435 10685 2438 0.013840 0.003595 1986 1493 Paguio-DB23 7 781579 774912 19643 7020 0.010536 0.001445 6167 4687 Paguio-DB8 7 7807 7737 2313 143 0.032191 0.004986 88 48 Paguio-DE12 7 755 748 278 17 0.011831 0.003315 11 3 Paguio-DE21 7 811 800 275 20 0.026784 0.004606 16 1 Paguio-DE23 7 15892 15761 5274 260 0.017192 0.005258 181 94 Paguio-DE7 7 4388 4351 1282 70 0.029644 0.006671 38 11 Paguio-G88 7 271172 268785 30587 5185 0.011628 0.002733 4333 2244 Paguio-KB103 7 249943 247648 39282 4743 0.012045 0.002447 3971 2105 Paguio-KB106 7 151403 150232 25490 2711 0.012962 0.003432 2247 1328 Paguio-KB108 7 990078 979783 43178 9850 0.009832 0.001496 8706 6003 Paguio-KB79 7 401577 398195 37158 6660 0.011029 0.002206 5707 3974 Paguio-MB74 7 1722386 1705901 104957 17841 0.013298 0.001608 15068 5919 Paguio-MB77 7 1680862 1667111 83655 15843 0.012338 0.001434 13620 6302 Paguio-MB83 7 948932 940121 46475 10310 0.010885 0.001679 8938 5429 Paguio-MB88 7 3741 3711 1697 57 0.017794 0.004742 41 8 Paguio-NS24 7 988897 980048 21574 8247 0.009753 0.001253 7297 5435 Paguio-NS9 7 1712768 1698374 33808 10502 0.010304 0.001018 9322 6356 Paguio-RB20 7 810487 802906 73067 10828 0.013892 0.002174 9082 5241 Paguio-RB35 7 547444 542836 70881 9543 0.012560 0.003105 7856 3831 Paguio-RB36 7 169183 167460 43035 3842 0.012928 0.003248 3161 1250 ## Alignment matrix statistics: snps matrix size: (24, 16471), 65.89% missing sites. sequence matrix size: (24, 1927707), 62.48% missing sites.