## 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 141779 filtered_by_rm_duplicates 2169 2169 139610 filtered_by_max_indels 5691 5691 133919 filtered_by_max_SNPs 28 1 133918 filtered_by_max_shared_het 4624 3763 130155 filtered_by_min_sample 16636 16636 113519 total_filtered_loci 29148 28260 113519 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage AA-021_NT 69203 AA-025_NT 62779 AA-026_TOL 68250 AA-034_NT 79441 AA-035_NT 9 AA-048_TOL 87056 AA-051_TOL 76152 AA-065_NT 77206 AA-069_NT 65055 AA-081_TOL 83781 AA-087_NT 80281 AA-125_NT 85922 AA-137_NT 81587 LAB_ID_224_TOL 83375 LAB_ID_229_TOL 87002 LAB_ID_230_TOL 82047 LAB_ID_238_TOL 84592 LAB_ID_250_TOL 82156 LAB_ID_252_TOL 85809 LAB_ID_269_TOL 88704 LAB_ID_284_NT 80436 LAB_ID_305_TOL 77363 LAB_ID_343_NT 88853 LAB_ID_349_NT 85300 ## 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 4910 4910 5 4508 9418 6 3801 13219 7 3542 16761 8 3438 20199 9 3613 23812 10 3701 27513 11 4074 31587 12 4296 35883 13 4558 40441 14 4478 44919 15 4430 49349 16 4065 53414 17 3920 57334 18 3419 60753 19 3251 64004 20 3397 67401 21 3799 71200 22 5266 76466 23 37048 113514 24 5 113519 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 90007 0 97754 0 1 17321 17321 12215 12215 2 3890 25101 2341 16897 3 1080 28341 631 18790 4 463 30193 236 19734 5 214 31263 91 20189 6 102 31875 53 20507 7 59 32288 27 20696 8 70 32848 32 20952 9 36 33172 21 21141 10 41 33582 12 21261 11 30 33912 12 21393 12 21 34164 18 21609 13 14 34346 10 21739 14 10 34486 6 21823 15 14 34696 3 21868 16 10 34856 5 21948 17 11 35043 6 22050 18 8 35187 4 22122 19 1 35206 2 22160 20 13 35466 6 22280 21 9 35655 3 22343 22 4 35743 4 22431 23 8 35927 4 22523 24 4 36023 2 22571 25 10 36273 5 22696 26 4 36377 6 22852 27 11 36674 4 22960 28 9 36926 3 23044 29 7 37129 1 23073 30 1 37159 0 23073 31 3 37252 1 23104 32 2 37316 0 23104 33 2 37382 0 23104 34 1 37416 0 23104 35 3 37521 0 23104 36 4 37665 1 23140 37 3 37776 0 23140 38 3 37890 0 23140 39 3 38007 0 23140 40 5 38207 0 23140 41 0 38207 0 23140 42 0 38207 0 23140 43 2 38293 0 23140 44 0 38293 0 23140 45 0 38293 0 23140 46 1 38339 0 23140 47 1 38386 0 23140 48 0 38386 0 23140 49 0 38386 0 23140 50 3 38536 0 23140 51 1 38587 0 23140 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly AA-021_NT 7 11689941 11527173 365223 96516 0.002140 0.001381 92919 69203 AA-025_NT 7 8706993 8598244 239363 73097 0.002149 0.001336 70395 62779 AA-026_TOL 7 9656295 9524013 286383 80411 0.002291 0.001381 77354 68250 AA-034_NT 7 12791797 12637447 297241 92168 0.002096 0.001277 88780 79441 AA-035_NT 7 55625 54852 14199 290 0.039658 0.013576 108 9 AA-048_TOL 7 16641734 16437579 317564 101648 0.002318 0.001300 97458 87056 AA-051_TOL 7 12714956 12534499 286878 88805 0.002448 0.001277 85241 76152 AA-065_NT 7 12542287 12375764 301164 89782 0.002219 0.001351 86243 77206 AA-069_NT 7 10157867 10015591 365177 84109 0.002138 0.001401 80793 65055 AA-081_TOL 7 17600122 17378958 379071 98112 0.002620 0.001352 93673 83781 AA-087_NT 7 14342626 14139322 329521 93967 0.002474 0.001384 90047 80281 AA-125_NT 7 16544897 16343145 359685 100308 0.002207 0.001243 96326 85922 AA-137_NT 7 16554552 16350914 481753 96882 0.002383 0.001213 92718 81587 LAB_ID_224_TOL 7 15752077 15559484 310055 97130 0.002159 0.001311 93121 83375 LAB_ID_229_TOL 7 16791901 16555098 316826 101723 0.002304 0.001269 97401 87002 LAB_ID_230_TOL 7 15200784 15001745 310162 95771 0.002314 0.001330 91706 82047 LAB_ID_238_TOL 7 15523077 15310245 316701 98637 0.002174 0.001328 94615 84592 LAB_ID_250_TOL 7 15314407 15127273 333821 97185 0.002249 0.001294 93111 82156 LAB_ID_252_TOL 7 16469061 16240644 334800 100443 0.002046 0.001345 96119 85809 LAB_ID_269_TOL 7 18287927 18066138 368930 104470 0.002342 0.001234 100021 88704 LAB_ID_284_NT 7 15847122 15654890 398248 94240 0.002114 0.001196 90177 80436 LAB_ID_305_TOL 7 13234714 13070417 361792 95133 0.002317 0.001352 91472 77363 LAB_ID_343_NT 7 16491590 16254133 324729 103706 0.002538 0.001285 99526 88853 LAB_ID_349_NT 7 15086743 14885926 335512 100113 0.002346 0.001324 96106 85300 ## Alignment matrix statistics: snps matrix size: (24, 38587), 36.41% missing sites. sequence matrix size: (24, 25696507), 28.09% missing sites.