## 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 0 160 filtered_by_rm_duplicates 3 3 157 filtered_by_max_indels 5 5 152 filtered_by_max_SNPs 0 0 152 filtered_by_max_shared_het 8 8 144 filtered_by_min_sample 89 89 55 total_filtered_loci 105 105 55 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage KLU334 16 KLU95 18 KLU96 15 KLU98 19 ODE1 14 ODE14 7 ODE30 25 ODE36 21 ODE40 18 ODE56 23 SADAu12 11 SADAu7 11 SCA1 12 SCA101 10 SCA2 6 SCA85 1 SCA87 1 SCA94 21 TAS20 21 TAS21 18 VEN16 16 VEN5 2 VEN89 13 VEN96 14 ## 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 24 24 5 5 29 6 5 34 7 7 41 8 6 47 9 3 50 10 4 54 11 0 54 12 0 54 13 0 54 14 0 54 15 0 54 16 0 54 17 0 54 18 1 55 19 0 55 20 0 55 21 0 55 22 0 55 23 0 55 24 0 55 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 8 0 21 0 1 13 13 9 9 2 3 19 8 25 3 6 37 1 28 4 1 41 4 44 5 0 41 5 69 6 3 59 0 69 7 6 101 2 83 8 3 125 0 83 9 3 152 1 92 10 0 152 1 102 11 0 152 0 102 12 0 152 1 114 13 2 178 0 114 14 1 192 1 128 15 0 192 0 128 16 0 192 0 128 17 2 226 0 128 18 0 226 1 146 19 0 226 0 146 20 0 226 0 146 21 0 226 0 146 22 0 226 0 146 23 1 249 0 146 24 0 249 0 146 25 1 274 0 146 26 0 274 0 146 27 0 274 0 146 28 0 274 0 146 29 0 274 0 146 30 0 274 0 146 31 1 305 0 146 32 0 305 0 146 33 0 305 0 146 34 0 305 0 146 35 0 305 0 146 36 0 305 0 146 37 0 305 0 146 38 1 343 0 146 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly KLU334 7 8952 8872 4977 56 0.018069 0.006335 40 16 KLU95 7 12242 12102 5866 86 0.020807 0.005376 51 18 KLU96 7 12780 12639 6227 77 0.019695 0.006631 48 15 KLU98 7 12983 12848 7227 73 0.021419 0.006686 48 19 ODE1 7 9156 9058 4975 63 0.025020 0.007096 39 14 ODE14 7 5713 5647 2977 33 0.021280 0.006537 22 7 ODE30 7 14948 14784 7173 96 0.019896 0.006287 67 25 ODE36 7 16186 16011 7102 99 0.027102 0.005367 54 21 ODE40 7 16858 16671 7665 91 0.021136 0.006978 59 18 ODE56 7 17642 17440 8042 119 0.023680 0.005730 82 23 SADAu12 7 5415 5359 2648 31 0.022108 0.001610 23 11 SADAu7 7 4386 4326 2425 39 0.019500 0.008840 25 11 SCA1 7 9930 9862 4974 50 0.016940 0.009604 34 12 SCA101 7 6264 6183 3227 28 0.019527 0.007534 18 10 SCA2 7 8873 8805 4659 36 0.022877 0.005725 18 6 SCA85 7 65 63 40 2 0.042566 0.014730 2 1 SCA87 7 58 58 25 2 0.038093 0.016114 1 1 SCA94 7 10345 10219 5155 73 0.023654 0.004657 49 21 TAS20 7 19786 19613 9181 130 0.022997 0.005326 88 21 TAS21 7 12203 12056 6445 72 0.020247 0.006425 51 18 VEN16 7 14452 14312 6721 91 0.021742 0.007726 57 16 VEN5 7 1561 1543 1012 9 0.014446 0.006239 5 2 VEN89 7 6706 6623 3498 32 0.020292 0.010726 23 13 VEN96 7 11042 10940 5528 63 0.025229 0.009050 40 14 ## Alignment matrix statistics: snps matrix size: (24, 343), 79.45% missing sites. sequence matrix size: (24, 11260), 76.67% missing sites.