## 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 136578 filtered_by_rm_duplicates 2286 2286 134292 filtered_by_max_indels 2160 2160 132132 filtered_by_max_SNPs 10346 9833 122299 filtered_by_max_shared_het 436 315 121984 filtered_by_min_sample 70418 70418 51566 total_filtered_loci 85646 85012 51566 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage Carex-MOR-3075_dup2trim 12606 Carex-MOR-3098_dup2trim 15151 Carex_MOR_3067_trim 14647 Carex_MOR_3068_trim 24504 Carex_MOR_3069_3126_trim 14713 Carex_MOR_3070_trim 24659 Carex_MOR_3071_3127_trim 20993 Carex_MOR_3072_trim 24830 Carex_MOR_3074_trim 26918 Carex_MOR_3075_trim 27350 Carex_MOR_3076_trim 26935 Carex_MOR_3078_trim 26285 Carex_MOR_3079_trim 23362 Carex_MOR_3080_trim 26870 Carex_MOR_3081_trim 27391 Carex_MOR_3082_trim 12748 Carex_MOR_3083_trim 25760 Carex_MOR_3084_3143_3130_trim 16086 Carex_MOR_3085_trim 23699 Carex_MOR_3087_trim 22551 Carex_MOR_3088_trim 26040 Carex_MOR_3089_trim 22056 Carex_MOR_3090_trim 23235 Carex_MOR_3091_trim 28908 Carex_MOR_3092_trim 29332 Carex_MOR_3093_trim 28665 Carex_MOR_3094_trim 27083 Carex_MOR_3095_trim 30360 Carex_MOR_3096_trim 29022 Carex_MOR_3097_trim 16847 Carex_MOR_3098_trim 30609 Carex_MOR_3099_trim 25653 Carex_MOR_3100_trim 27923 Carex_MOR_3102_trim 25537 Carex_MOR_3104_trim 28388 Carex_MOR_3105_trim 30159 Carex_MOR_3106_trim 27475 Carex_MOR_3107_trim 26544 Carex_MOR_3108_trim 25573 Carex_MOR_3110_trim 27664 Carex_MOR_3111_3135_trim 18292 Carex_MOR_3113_3137_trim 7685 Carex_MOR_3116_trim 12695 Carex_MOR_3117_trim 21506 Carex_MOR_3119_trim 26908 Carex_MOR_3125_trim 18675 Carex_MOR_3128_trim 24512 Carex_MOR_3129_trim 20479 Carex_MOR_3131_trim 18929 Carex_MOR_3132_trim 23702 Carex_MOR_3134_trim 23534 Carex_MOR_3140_trim 20011 Carex_MOR_3E1_JMC17trim 9521 Carex_MOR_8E1_JMC17trim 7376 ## 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 0 0 5 0 0 6 4354 4354 7 3393 7747 8 2883 10630 9 2463 13093 10 2286 15379 11 2125 17504 12 1906 19410 13 1575 20985 14 1290 22275 15 1070 23345 16 1030 24375 17 969 25344 18 878 26222 19 727 26949 20 661 27610 21 609 28219 22 600 28819 23 571 29390 24 555 29945 25 542 30487 26 575 31062 27 585 31647 28 562 32209 29 555 32764 30 594 33358 31 581 33939 32 535 34474 33 543 35017 34 542 35559 35 550 36109 36 516 36625 37 548 37173 38 586 37759 39 588 38347 40 612 38959 41 630 39589 42 765 40354 43 865 41219 44 995 42214 45 1171 43385 46 1279 44664 47 1447 46111 48 1540 47651 49 1448 49099 50 1170 50269 51 762 51031 52 372 51403 53 133 51536 54 30 51566 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 1974 0 6640 0 1 2261 2261 6913 6913 2 2417 7095 7015 20943 3 2649 15042 6941 41766 4 2791 26206 6326 67070 5 2842 40416 5511 94625 6 2932 58008 4294 120389 7 3086 79610 3168 142565 8 3176 105018 2215 160285 9 3400 135618 1301 171994 10 3385 169468 732 179314 11 3377 206615 314 182768 12 3327 246539 125 184268 13 3171 287762 54 184970 14 2948 329034 9 185096 15 2752 370314 7 185201 16 2530 410794 0 185201 17 2196 448126 1 185218 18 294 453418 0 185218 19 29 453969 0 185218 20 14 454249 0 185218 21 6 454375 0 185218 22 5 454485 0 185218 23 2 454531 0 185218 24 1 454555 0 185218 25 1 454580 0 185218 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly Carex-MOR-3075_dup2trim 7 1222538 1222208 33902 25797 0.002630 0.000971 25411 12606 Carex-MOR-3098_dup2trim 7 1238465 1238095 29927 23047 0.003693 0.001044 22527 15151 Carex_MOR_3067_trim 7 1281387 975380 83797 37955 0.003214 0.000576 37019 14647 Carex_MOR_3068_trim 7 1783664 1533240 106258 52529 0.002779 0.000596 51435 24504 Carex_MOR_3069_3126_trim 7 917913 600787 83044 32491 0.004775 0.000867 31439 14713 Carex_MOR_3070_trim 7 2008839 1797680 148869 64557 0.003817 0.000662 62875 24659 Carex_MOR_3071_3127_trim 7 1265933 1048766 111732 46025 0.002844 0.000723 44956 20993 Carex_MOR_3072_trim 7 2002138 1658484 103281 50868 0.003883 0.000628 49615 24830 Carex_MOR_3074_trim 7 1880318 1722056 69169 43724 0.003193 0.000631 42578 26918 Carex_MOR_3075_trim 7 2626989 2421517 151371 61389 0.003525 0.000580 59653 27350 Carex_MOR_3076_trim 7 2049828 1821329 83498 46368 0.003623 0.000657 45107 26935 Carex_MOR_3078_trim 7 1959595 1693831 112397 52084 0.003481 0.000705 50715 26285 Carex_MOR_3079_trim 7 1408796 1042522 90443 44132 0.003668 0.000692 43000 23362 Carex_MOR_3080_trim 7 2148857 1849726 109155 51286 0.004619 0.000709 49822 26870 Carex_MOR_3081_trim 7 3222740 2930426 102708 53010 0.007284 0.000597 51059 27391 Carex_MOR_3082_trim 7 2055278 1891227 276576 94632 0.012385 0.002504 86041 12748 Carex_MOR_3083_trim 7 1597061 1378834 86685 46422 0.005018 0.000753 44903 25760 Carex_MOR_3084_3143_3130_trim 7 1166134 786773 82190 37163 0.003908 0.000736 36135 16086 Carex_MOR_3085_trim 7 1683408 1318956 152756 58618 0.006996 0.000901 55660 23699 Carex_MOR_3087_trim 7 1180303 974707 78067 40278 0.005861 0.001030 38525 22551 Carex_MOR_3088_trim 7 1675957 1459939 88001 47873 0.005108 0.000840 46190 26040 Carex_MOR_3089_trim 7 1759544 1451561 92630 47587 0.007539 0.000749 45761 22056 Carex_MOR_3090_trim 7 1501248 1102480 92383 44239 0.007460 0.000909 42326 23235 Carex_MOR_3091_trim 7 1703120 1496089 126261 55499 0.003989 0.000806 53853 28908 Carex_MOR_3092_trim 7 1841939 1592557 86139 47054 0.004310 0.000732 45461 29332 Carex_MOR_3093_trim 7 2621192 2377342 228926 81705 0.004886 0.000781 78273 28665 Carex_MOR_3094_trim 7 1809331 1597173 122378 55814 0.003467 0.000727 54308 27083 Carex_MOR_3095_trim 7 2508828 2051500 84853 47900 0.004101 0.000745 46276 30360 Carex_MOR_3096_trim 7 2564733 2313519 76065 46686 0.003860 0.000647 45111 29022 Carex_MOR_3097_trim 7 755262 543216 64876 29131 0.005355 0.001003 28010 16847 Carex_MOR_3098_trim 7 2388070 2072732 73977 46567 0.004244 0.000660 44998 30609 Carex_MOR_3099_trim 7 1466048 1323687 71127 42132 0.006461 0.000930 40455 25653 Carex_MOR_3100_trim 7 1995043 1772783 122108 56167 0.007879 0.001045 53542 27923 Carex_MOR_3102_trim 7 1570160 1326148 78048 45824 0.005979 0.000925 44070 25537 Carex_MOR_3104_trim 7 1413989 1250119 82840 46529 0.005675 0.000923 44788 28388 Carex_MOR_3105_trim 7 2338748 1885511 77106 46561 0.004515 0.000718 44975 30159 Carex_MOR_3106_trim 7 2035897 1830468 144021 59681 0.004452 0.000848 57495 27475 Carex_MOR_3107_trim 7 1723007 1578548 127812 55253 0.004584 0.000788 53395 26544 Carex_MOR_3108_trim 7 1440882 1266157 99859 48043 0.004227 0.000796 46461 25573 Carex_MOR_3110_trim 7 1997567 1787442 81395 48046 0.004268 0.000718 46415 27664 Carex_MOR_3111_3135_trim 7 1045109 786365 60230 34065 0.004468 0.000738 33103 18292 Carex_MOR_3113_3137_trim 7 531364 351185 72749 19238 0.007148 0.001317 18293 7685 Carex_MOR_3116_trim 7 737241 485940 78637 27014 0.006853 0.001462 25731 12695 Carex_MOR_3117_trim 7 1137246 1023049 111875 46708 0.006349 0.001059 44580 21506 Carex_MOR_3119_trim 7 1712213 1478867 115508 52493 0.004822 0.000837 50681 26908 Carex_MOR_3125_trim 7 999189 870096 57178 35844 0.003376 0.000767 34990 18675 Carex_MOR_3128_trim 7 1615977 1317503 70350 43049 0.005385 0.000626 41755 24512 Carex_MOR_3129_trim 7 1352802 1157068 83656 44013 0.004978 0.000733 42802 20479 Carex_MOR_3131_trim 7 1313196 941153 149921 51548 0.005608 0.000823 49427 18929 Carex_MOR_3132_trim 7 1209440 1053301 99018 46512 0.004242 0.000857 45211 23702 Carex_MOR_3134_trim 7 1353271 925107 80777 41317 0.005139 0.000963 39912 23534 Carex_MOR_3140_trim 7 871372 762545 59252 34768 0.005166 0.001053 33454 20011 Carex_MOR_3E1_JMC17trim 7 907210 906963 24832 18887 0.003000 0.000966 18521 9521 Carex_MOR_8E1_JMC17trim 7 655359 655199 21422 16165 0.002074 0.000950 15969 7376 ## Alignment matrix statistics: snps matrix size: (54, 454580), 48.22% missing sites. sequence matrix size: (54, 4478844), 56.58% missing sites.