## 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 23 filtered_by_rm_duplicates 0 0 23 filtered_by_max_indels 3 3 20 filtered_by_max_SNPs 0 0 20 filtered_by_max_shared_het 1 1 19 filtered_by_min_sample 8 8 11 total_filtered_loci 12 12 11 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage FA326_CL_Weiss 6 FA328_CL_Weiss 6 FA335_CV_Weiss 5 FA380_CL_Peachtree 4 FA382_CL_Peachtree 7 FA391_CH_Weiss 7 FA397_CV_Weiss 4 FA407_CH_Coosae 6 FA409_CH_Coosae 7 FA420_CL_Peachtree 9 FA421_CL_Peachtree 7 FA434_CL_Turkey 8 FA436_CL_Turkey 1 FA438_CL_Turkey 5 FA470_CV_Coosae2 6 FA471_CV_Coosae2 6 FA474_CL_Weiss 8 FA475_CL_Weiss 1 FA493_CV_Conasauga 5 FA501_CV_Conasauga 1 ## 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 1 1 5 0 1 6 0 1 7 2 3 8 0 3 9 1 4 10 4 8 11 1 9 12 0 9 13 0 9 14 0 9 15 1 10 16 1 11 17 0 11 18 0 11 19 0 11 20 0 11 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 2 0 4 0 1 1 1 2 2 2 2 5 1 4 3 1 8 0 4 4 0 8 1 8 5 0 8 1 13 6 1 14 0 13 7 1 21 0 13 8 0 21 0 13 9 1 30 1 22 10 0 30 0 22 11 2 52 1 33 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly FA326_CL_Weiss 7 2615 2590 1565 14 0.008460 0.004623 12 6 FA328_CL_Weiss 7 2267 2249 1347 9 0.002000 0.004719 9 6 FA335_CV_Weiss 7 3642 3601 2330 19 0.023157 0.003832 12 5 FA380_CL_Peachtree 7 1563 1542 981 7 0.007113 0.005041 6 4 FA382_CL_Peachtree 7 3473 3444 1939 17 0.008890 0.003241 15 7 FA391_CH_Weiss 7 1890 1873 1245 13 0.016541 0.002567 9 7 FA397_CV_Weiss 7 1839 1813 1271 7 0.008922 0.002962 5 4 FA407_CH_Coosae 7 2064 2032 1375 12 0.017839 0.003969 9 6 FA409_CH_Coosae 7 2650 2619 1769 17 0.005927 0.004173 13 7 FA420_CL_Peachtree 7 5381 5328 2876 29 0.013432 0.003660 22 9 FA421_CL_Peachtree 7 3176 3141 1885 16 0.009500 0.004500 13 7 FA434_CL_Turkey 7 2067 2050 1365 13 0.007692 0.004783 12 8 FA436_CL_Turkey 7 339 337 225 2 0.003412 0.005424 2 1 FA438_CL_Turkey 7 2161 2131 1334 9 0.006289 0.004118 8 5 FA470_CV_Coosae2 7 3714 3683 2389 23 0.015421 0.004416 15 6 FA471_CV_Coosae2 7 903 895 629 7 0.005145 0.002639 6 6 FA474_CL_Weiss 7 2708 2671 1628 18 0.009436 0.004510 13 8 FA475_CL_Weiss 7 56 56 11 1 0.003828 0.014714 1 1 FA493_CV_Conasauga 7 1766 1753 1243 7 0.010664 0.002439 6 5 FA501_CV_Conasauga 7 256 254 183 1 0.000381 0.003144 1 1 ## Alignment matrix statistics: snps matrix size: (20, 52), 51.73% missing sites. sequence matrix size: (20, 2776), 51.84% missing sites.