## 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 36178 filtered_by_rm_duplicates 575 575 35603 filtered_by_max_indels 5215 5215 30388 filtered_by_max_SNPs 117 39 30349 filtered_by_max_shared_het 990 787 29562 filtered_by_min_sample 17152 17152 12410 total_filtered_loci 24049 23768 12410 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage SG-01 6532 SG-02 6034 SG-03 5844 SG-04 4913 SG-05 3436 SG-06 3377 SG-07 4683 SG-08 1703 SG-09 3792 SG-10 2938 SG-11 2876 SG-12 4140 SG-13 3538 SG-14 4997 SG-15 5259 SG-16 4049 SG-17 3545 SG-18 2114 SG-19 4250 SG-20 5602 SG-21 3202 SG-22 3600 SG-23 5775 SG-24 5747 ## 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 2933 2933 5 1949 4882 6 1515 6397 7 1053 7450 8 883 8333 9 711 9044 10 586 9630 11 449 10079 12 321 10400 13 264 10664 14 199 10863 15 196 11059 16 159 11218 17 148 11366 18 164 11530 19 168 11698 20 163 11861 21 159 12020 22 147 12167 23 133 12300 24 110 12410 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 1293 0 3554 0 1 1077 1077 1746 1746 2 872 2821 1281 4308 3 809 5248 1034 7410 4 737 8196 813 10662 5 656 11476 727 14297 6 568 14884 538 17525 7 543 18685 485 20920 8 498 22669 367 23856 9 510 27259 346 26970 10 430 31559 265 29620 11 434 36333 206 31886 12 352 40557 166 33878 13 390 45627 143 35737 14 334 50303 104 37193 15 295 54728 105 38768 16 250 58728 83 40096 17 249 62961 72 41320 18 223 66975 62 42436 19 193 70642 41 43215 20 171 74062 30 43815 21 136 76918 40 44655 22 144 80086 22 45139 23 144 83398 11 45392 24 117 86206 22 45920 25 104 88806 6 46070 26 72 90678 22 46642 27 82 92892 13 46993 28 62 94628 10 47273 29 55 96223 11 47592 30 50 97723 8 47832 31 40 98963 7 48049 32 42 100307 11 48401 33 48 101891 7 48632 34 35 103081 10 48972 35 32 104201 6 49182 36 35 105461 8 49470 37 34 106719 7 49729 38 26 107707 4 49881 39 21 108526 2 49959 40 27 109606 2 50039 41 21 110467 3 50162 42 26 111559 4 50330 43 22 112505 4 50502 44 19 113341 0 50502 45 15 114016 0 50502 46 10 114476 0 50502 47 20 115416 2 50596 48 15 116136 0 50596 49 12 116724 0 50596 50 10 117224 0 50596 51 8 117632 0 50596 52 4 117840 0 50596 53 10 118370 0 50596 54 7 118748 0 50596 55 4 118968 0 50596 56 10 119528 0 50596 57 4 119756 0 50596 58 3 119930 0 50596 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly SG-01 7 1746394 1732389 97471 21009 0.027067 0.004198 15682 6532 SG-02 7 1485806 1472088 94580 18930 0.028448 0.004192 13787 6034 SG-03 7 1973991 1957131 104641 23639 0.030196 0.005362 16763 5844 SG-04 7 1661403 1645858 89697 21181 0.028270 0.004560 16013 4913 SG-05 7 1356784 1345958 80793 15348 0.028055 0.004217 11421 3436 SG-06 7 755871 748445 61115 10546 0.027126 0.004088 7989 3377 SG-07 7 937848 930584 69900 12639 0.028354 0.003835 9501 4683 SG-08 7 352952 350069 43621 5622 0.028232 0.004261 4196 1703 SG-09 7 1470914 1456826 89241 18600 0.028783 0.005694 13628 3792 SG-10 7 859410 850084 68798 12131 0.028169 0.004306 9089 2938 SG-11 7 792615 784613 54689 8457 0.028889 0.004196 5633 2876 SG-12 7 879716 869592 79603 11298 0.030991 0.004832 7740 4140 SG-13 7 682568 675949 58737 9120 0.027216 0.004702 6470 3538 SG-14 7 1467026 1448434 108172 19289 0.031702 0.006115 12382 4997 SG-15 7 1201168 1190580 87059 13960 0.032383 0.004620 10067 5259 SG-16 7 1109324 1098440 86609 13992 0.032377 0.005001 8665 4049 SG-17 7 748258 741695 54392 8832 0.026358 0.003854 6424 3545 SG-18 7 362284 358538 38910 5313 0.027110 0.004240 3872 2114 SG-19 7 1001916 992194 78524 13740 0.031063 0.005322 9268 4250 SG-20 7 1575788 1559355 89768 17857 0.029489 0.004426 13060 5602 SG-21 7 684163 677984 61110 9849 0.029604 0.004785 6217 3202 SG-22 7 675707 668506 55790 8978 0.024033 0.003674 6528 3600 SG-23 7 1417233 1405146 101613 18959 0.031762 0.005511 13126 5775 SG-24 7 1314068 1302180 107246 17530 0.027374 0.005591 12177 5747 ## Alignment matrix statistics: snps matrix size: (24, 119930), 64.76% missing sites. sequence matrix size: (24, 3401733), 65.94% missing sites.