## 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 72707 filtered_by_rm_duplicates 2303 2303 70404 filtered_by_max_indels 11425 11425 58979 filtered_by_max_SNPs 15 2 58977 filtered_by_max_shared_het 2193 1521 57456 filtered_by_min_sample 18910 18910 38546 total_filtered_loci 34846 34161 38546 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage BYC2 21023 BYC8 14787 BYC9 15464 CMC11 20250 CMC3 20795 CMC8 20709 DKC5 21641 DKC6 19835 DKC7 21714 KDC11 20263 KDC9 21408 LAC2 136 LAC3 22669 LAC4 22434 LGC2 11 LGC5 17304 LGC8 21243 ODC10 20989 ODC14 7 ODC16 20830 ODC6 21448 SAC16 14822 SAC17 19195 SAC6 22089 ## 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 4643 4643 5 3541 8184 6 3117 11301 7 2763 14064 8 2660 16724 9 2349 19073 10 2105 21178 11 1581 22759 12 1566 24325 13 1414 25739 14 1389 27128 15 1297 28425 16 1414 29839 17 1452 31291 18 1563 32854 19 1654 34508 20 1915 36423 21 2068 38491 22 53 38544 23 1 38545 24 1 38546 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 7017 0 11759 0 1 4484 4484 5417 5417 2 3929 12342 4284 13985 3 3232 22038 3383 24134 4 2921 33722 2670 34814 5 2495 46197 2112 45374 6 2230 59577 1802 56186 7 1924 73045 1494 66644 8 1694 86597 1168 75988 9 1379 99008 921 84277 10 1187 110878 782 92097 11 986 121724 610 98807 12 897 132488 508 104903 13 768 142472 358 109557 14 553 150214 285 113547 15 540 158314 201 116562 16 405 164794 190 119602 17 354 170812 136 121914 18 261 175510 114 123966 19 233 179937 72 125334 20 183 183597 65 126634 21 176 187293 50 127684 22 124 190021 44 128652 23 112 192597 30 129342 24 85 194637 24 129918 25 65 196262 15 130293 26 55 197692 16 130709 27 54 199150 10 130979 28 36 200158 7 131175 29 30 201028 4 131291 30 32 201988 6 131471 31 14 202422 3 131564 32 13 202838 2 131628 33 13 203267 3 131727 34 13 203709 0 131727 35 12 204129 0 131727 36 7 204381 0 131727 37 8 204677 0 131727 38 8 204981 1 131765 39 2 205059 0 131765 40 4 205219 0 131765 41 1 205260 0 131765 42 3 205386 0 131765 43 1 205429 0 131765 44 0 205429 0 131765 45 0 205429 0 131765 46 1 205475 0 131765 47 0 205475 0 131765 48 0 205475 0 131765 49 0 205475 0 131765 50 0 205475 0 131765 51 1 205526 0 131765 52 0 205526 0 131765 53 1 205579 0 131765 54 2 205687 0 131765 55 1 205742 0 131765 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly BYC2 7 2785024 2745847 113042 36389 0.006729 0.001350 34365 21023 BYC8 7 1189677 1176107 78431 24579 0.007300 0.001447 23396 14787 BYC9 7 2864124 2815566 108338 33119 0.005957 0.001600 31266 15464 CMC11 7 1980485 1952782 91178 32507 0.006871 0.001539 30891 20250 CMC3 7 2472384 2438394 112407 33794 0.006686 0.001528 32069 20795 CMC8 7 2750015 2714465 102593 34763 0.006412 0.001359 33108 20709 DKC5 7 3560118 3508612 110096 37008 0.006747 0.001347 34932 21641 DKC6 7 6886734 6788501 260865 36906 0.007829 0.001144 34166 19835 DKC7 7 4476127 4418345 132686 37611 0.006671 0.001377 35403 21714 KDC11 7 2452191 2419734 110933 34257 0.006772 0.001346 32581 20263 KDC9 7 3979972 3929621 137884 36677 0.006971 0.001309 34655 21408 LAC2 7 28341 27956 15394 331 0.014559 0.005866 249 136 LAC3 7 3260147 3222388 111739 36961 0.006500 0.001285 35103 22669 LAC4 7 3043902 3006556 113845 36814 0.006389 0.001324 35025 22434 LGC2 7 12743 12552 8802 55 0.026792 0.012578 25 11 LGC5 7 1553439 1533544 77973 28711 0.007113 0.001477 27282 17304 LGC8 7 3597264 3553740 127747 37236 0.006787 0.001364 35177 21243 ODC10 7 2652119 2613716 105377 35527 0.006990 0.001406 33724 20989 ODC14 7 7052 6933 5375 31 0.029539 0.013384 18 7 ODC16 7 3490642 3440778 152735 34311 0.006105 0.001411 32515 20830 ODC6 7 2660149 2625237 107380 34781 0.006172 0.001631 33040 21448 SAC16 7 1535398 1515531 131609 24895 0.005792 0.001388 23718 14822 SAC17 7 2663560 2630124 145783 31638 0.006563 0.001407 30041 19195 SAC6 7 3872775 3826566 124346 36885 0.006204 0.001174 34994 22089 ## Alignment matrix statistics: snps matrix size: (24, 205742), 47.04% missing sites. sequence matrix size: (24, 8200948), 54.75% missing sites.