## 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 50614 filtered_by_rm_duplicates 1568 1568 49046 filtered_by_max_indels 2205 2205 46841 filtered_by_max_SNPs 19 6 46835 filtered_by_max_shared_het 1220 1033 45802 filtered_by_min_sample 22493 22493 23309 total_filtered_loci 27505 27305 23309 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage CT1-8PA 16952 IL1-16PB 16474 MD5-P4B 11560 NC16-22PC 13911 NJ1-15PA 4921 NY5-15PA 18167 PA1-8PA 14812 PATH1-7_PAR_A 16115 PCQ2-13A 17490 PHN3-24 16456 PHU6-1A 16931 PJP10-16A 14969 PJP11-15A 15761 PJP5-16A 14874 PJP9-13 14803 PJix1-13A 9571 PKO1-13A 17321 PKO14-24 16084 PKO2-19 15755 PSC1-13 15345 PTW1-26 10195 PZJ4-16A 15414 RI2-P25C 9173 SC7-11PA 16265 ## 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 2823 2823 5 1516 4339 6 1053 5392 7 855 6247 8 655 6902 9 536 7438 10 457 7895 11 477 8372 12 492 8864 13 491 9355 14 570 9925 15 676 10601 16 721 11322 17 796 12118 18 985 13103 19 1093 14196 20 1193 15389 21 1481 16870 22 1333 18203 23 2540 20743 24 2566 23309 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 11600 0 16203 0 1 5721 5721 4093 4093 2 2582 10885 1456 7005 3 1146 14323 559 8682 4 602 16731 300 9882 5 330 18381 158 10672 6 198 19569 88 11200 7 162 20703 93 11851 8 105 21543 51 12259 9 85 22308 45 12664 10 78 23088 39 13054 11 57 23715 26 13340 12 61 24447 37 13784 13 58 25201 27 14135 14 63 26083 17 14373 15 39 26668 8 14493 16 32 27180 9 14637 17 29 27673 6 14739 18 19 28015 6 14847 19 18 28357 8 14999 20 28 28917 7 15139 21 22 29379 9 15328 22 28 29995 4 15416 23 24 30547 14 15738 24 22 31075 11 16002 25 22 31625 7 16177 26 28 32353 11 16463 27 30 33163 11 16760 28 10 33443 3 16844 29 13 33820 2 16902 30 14 34240 0 16902 31 10 34550 0 16902 32 11 34902 0 16902 33 5 35067 0 16902 34 10 35407 0 16902 35 7 35652 0 16902 36 7 35904 0 16902 37 4 36052 0 16902 38 3 36166 1 16940 39 2 36244 0 16940 40 2 36324 0 16940 41 3 36447 0 16940 42 2 36531 0 16940 43 2 36617 0 16940 44 6 36881 0 16940 45 1 36926 0 16940 46 0 36926 0 16940 47 0 36926 0 16940 48 2 37022 0 16940 49 0 37022 0 16940 50 0 37022 0 16940 51 3 37175 0 16940 52 0 37175 0 16940 53 1 37228 0 16940 54 0 37228 0 16940 55 2 37338 0 16940 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly CT1-8PA 7 6014765 5964012 179058 46927 0.009319 0.001271 39946 16952 IL1-16PB 7 5162908 5122123 117442 30953 0.009073 0.001172 26857 16474 MD5-P4B 7 3180050 3150257 130773 36866 0.009943 0.001484 31917 11560 NC16-22PC 7 3310801 3281970 98631 23841 0.009889 0.001425 20367 13911 NJ1-15PA 7 2643844 2623717 70210 22215 0.007729 0.001332 19660 4921 NY5-15PA 7 6384319 6330120 163263 42506 0.009029 0.001238 36187 18167 PA1-8PA 7 3051364 3027167 91277 23965 0.009717 0.001448 21146 14812 PATH1-7_PAR_A 7 4288623 4244571 100768 25988 0.009297 0.001322 22701 16115 PCQ2-13A 7 5935267 5871130 113484 29869 0.008195 0.001472 26359 17490 PHN3-24 7 4104223 4062403 95798 25531 0.008232 0.001497 22514 16456 PHU6-1A 7 4516719 4473316 100201 26439 0.007900 0.001399 23422 16931 PJP10-16A 7 2875808 2847573 85982 22701 0.007840 0.001598 20411 14969 PJP11-15A 7 3671739 3635764 86102 23543 0.008629 0.001355 20847 15761 PJP5-16A 7 3430039 3392671 86502 22914 0.008961 0.001515 20211 14874 PJP9-13 7 3005811 2977162 84990 22681 0.008746 0.001506 20089 14803 PJix1-13A 7 1007225 997100 36059 12445 0.008626 0.001682 11238 9571 PKO1-13A 7 5912205 5853003 100348 27188 0.008588 0.001210 23773 17321 PKO14-24 7 3987342 3946846 82012 23700 0.008560 0.001436 21124 16084 PKO2-19 7 3527210 3492425 83273 23533 0.009055 0.001466 20919 15755 PSC1-13 7 4003338 3962929 98796 25009 0.009380 0.001488 21448 15345 PTW1-26 7 1095110 1082723 64602 15833 0.008283 0.001665 14384 10195 PZJ4-16A 7 4196985 4152084 120989 34964 0.007974 0.001531 31168 15414 RI2-P25C 7 2587084 2566262 151879 45722 0.009309 0.001524 39348 9173 SC7-11PA 7 5101693 5051864 95529 25715 0.008687 0.001348 22556 16265 ## Alignment matrix statistics: snps matrix size: (24, 37338), 51.19% missing sites. sequence matrix size: (24, 6198977), 36.40% missing sites.