## 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 55 filtered_by_rm_duplicates 3 3 52 filtered_by_max_indels 1 1 51 filtered_by_max_SNPs 0 0 51 filtered_by_max_shared_het 10 10 41 filtered_by_min_sample 18 18 23 total_filtered_loci 32 32 23 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage Angelito_L_U_10 13 Angelito_L_U_11 12 Angelito_L_U_12 10 Angelito_L_U_13 11 Angelito_L_U_8 9 Angelito_L_U_9 9 Carr9966E300_L_S_14 7 Carr9966E300_L_S_15 17 Carr9966E300_L_S_16 6 Carr9966E300_L_S_17 16 Carr9966E300_L_S_18 10 EastPeak_H_S_5 11 EastPeak_H_S_6 12 EastPeak_H_S_7 10 EastPeak_H_U_1 12 EastPeak_H_U_2 14 EastPeak_H_U_27 11 EastPeak_H_U_3 14 MtBritton_H_U_20 9 MtBritton_H_U_21 16 MtBritton_H_U_24 8 MtBritton_H_U_32 9 MtBritton_H_U_33 12 MtBritton_H_U_34 11 ## 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 6 6 5 1 7 6 2 9 7 2 11 8 2 13 9 1 14 10 0 14 11 0 14 12 0 14 13 0 14 14 0 14 15 0 14 16 1 15 17 0 15 18 0 15 19 2 17 20 0 17 21 2 19 22 1 20 23 1 21 24 2 23 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 4 0 9 0 1 4 4 7 7 2 4 12 2 11 3 4 24 1 14 4 1 28 0 14 5 2 38 3 29 6 0 38 0 29 7 1 45 0 29 8 1 53 0 29 9 0 53 0 29 10 0 53 0 29 11 0 53 0 29 12 1 65 0 29 13 0 65 0 29 14 0 65 1 43 15 0 65 0 43 16 1 81 0 43 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly Angelito_L_U_10 7 7388 7326 5068 44 0.030281 0.006456 24 13 Angelito_L_U_11 7 8388 8287 5769 44 0.027935 0.007692 26 12 Angelito_L_U_12 7 4298 4256 3107 27 0.027016 0.008286 17 10 Angelito_L_U_13 7 6966 6888 4782 38 0.029973 0.007574 22 11 Angelito_L_U_8 7 3586 3545 2580 20 0.025173 0.009987 12 9 Angelito_L_U_9 7 4678 4631 3268 26 0.026182 0.009946 16 9 Carr9966E300_L_S_14 7 2605 2568 1902 16 0.029537 0.013925 11 7 Carr9966E300_L_S_15 7 9138 9048 6218 52 0.034522 0.007610 30 17 Carr9966E300_L_S_16 7 2682 2652 1971 20 0.024113 0.007676 12 6 Carr9966E300_L_S_17 7 11865 11734 7732 63 0.021859 0.009452 35 16 Carr9966E300_L_S_18 7 6463 6389 4449 37 0.024556 0.009120 21 10 EastPeak_H_S_5 7 5105 5061 3602 27 0.026265 0.007769 15 11 EastPeak_H_S_6 7 8761 8672 5843 43 0.026265 0.008480 22 12 EastPeak_H_S_7 7 3829 3781 2681 23 0.030334 0.005741 16 10 EastPeak_H_U_1 7 4515 4470 3275 28 0.031231 0.007438 17 12 EastPeak_H_U_2 7 9603 9495 6448 47 0.029038 0.008373 26 14 EastPeak_H_U_27 7 6351 6278 4428 26 0.023606 0.006730 17 11 EastPeak_H_U_3 7 7777 7676 5207 35 0.029496 0.009697 23 14 MtBritton_H_U_20 7 4229 4183 3050 24 0.020285 0.007689 13 9 MtBritton_H_U_21 7 12883 12764 8378 72 0.028541 0.008090 40 16 MtBritton_H_U_24 7 4879 4811 3400 27 0.017841 0.010058 19 8 MtBritton_H_U_32 7 5317 5257 3717 25 0.032815 0.007916 12 9 MtBritton_H_U_33 7 5582 5515 3905 34 0.017301 0.010902 22 12 MtBritton_H_U_34 7 5509 5457 3887 29 0.035058 0.006507 19 11 ## Alignment matrix statistics: snps matrix size: (24, 81), 55.45% missing sites. sequence matrix size: (24, 4981), 48.65% missing sites.