## 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 129153 filtered_by_rm_duplicates 708 708 128445 filtered_by_max_indels 11520 11520 116925 filtered_by_max_SNPs 31 19 116906 filtered_by_max_shared_het 438 367 116539 filtered_by_min_sample 60073 60073 56466 total_filtered_loci 72770 72687 56466 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage UFMS5999 28684 UFPB80 296 UFRN9873 14181 UNB11151 31561 UNB14604 38924 UNB26041 33630 UNB26617 15656 UNB35336 32 UNB36738 19662 UNB37299 12039 UNB43656 3533 UNB44526 25943 UNB51175 12099 UNB55876 9282 UNB57752 18649 UNB65032 7602 UNB68414 26863 UNB7514 27787 UNB7601 2615 USP14202 23883 USP14838 18480 USP1674 23793 USP2902 1059 USP4000 6887 ## 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 12185 12185 5 9350 21535 6 7585 29120 7 6398 35518 8 5217 40735 9 4196 44931 10 3415 48346 11 2536 50882 12 1818 52700 13 1390 54090 14 1024 55114 15 620 55734 16 375 56109 17 206 56315 18 99 56414 19 39 56453 20 12 56465 21 1 56466 22 0 56466 23 0 56466 24 0 56466 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 0 838 0 10798 0 1 1871 1871 10341 10341 2 2865 7601 8688 27717 3 3604 18413 6814 48159 4 3914 34069 5220 69039 5 4189 55014 3911 88594 6 4159 79968 2934 106198 7 4067 108437 2277 122137 8 3985 140317 1618 135081 9 3529 172078 1122 145179 10 3236 204438 799 153169 11 2918 236536 577 159516 12 2558 267232 400 164316 13 2270 296742 270 167826 14 1924 323678 178 170318 15 1677 348833 149 172553 16 1445 371953 94 174057 17 1224 392761 76 175349 18 1014 411013 62 176465 19 834 426859 38 177187 20 743 441719 41 178007 21 611 454550 18 178385 22 538 466386 17 178759 23 455 476851 8 178943 24 361 485515 6 179087 25 309 493240 7 179262 26 243 499558 1 179288 27 182 504472 0 179288 28 160 508952 1 179316 29 134 512838 1 179345 30 117 516348 0 179345 31 95 519293 0 179345 32 73 521629 0 179345 33 78 524203 0 179345 34 52 525971 0 179345 35 48 527651 0 179345 36 24 528515 0 179345 37 22 529329 0 179345 38 16 529937 0 179345 39 19 530678 0 179345 40 21 531518 0 179345 41 10 531928 0 179345 42 5 532138 0 179345 43 9 532525 0 179345 44 5 532745 0 179345 45 2 532835 0 179345 46 6 533111 0 179345 47 3 533252 0 179345 48 3 533396 0 179345 49 0 533396 0 179345 50 1 533446 0 179345 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly UFMS5999 7 3851314 3804415 233747 81828 0.007860 0.001104 78492 28684 UFPB80 7 290572 286349 91649 6271 0.008276 0.001075 5763 296 UFRN9873 7 521400 515639 119917 25166 0.010247 0.001453 23313 14181 UNB11151 7 992512 982188 130774 54297 0.005610 0.001032 52203 31561 UNB14604 7 2077975 2056885 158372 79720 0.005122 0.000928 77033 38924 UNB26041 7 1105141 1094303 131713 60602 0.003768 0.001024 58762 33630 UNB26617 7 533531 527780 111926 25630 0.008821 0.001031 24265 15656 UNB35336 7 2141658 2112386 335100 86687 0.009833 0.001447 81113 32 UNB36738 7 641503 634418 120905 30625 0.009955 0.001117 28695 19662 UNB37299 7 432474 427917 102170 19202 0.009310 0.001135 18095 12039 UNB43656 7 221965 219214 78353 5380 0.017802 0.002317 4516 3533 UNB44526 7 860793 851848 123605 47477 0.004554 0.000963 45807 25943 UNB51175 7 449736 444909 106117 19220 0.011348 0.001229 17843 12099 UNB55876 7 353668 350312 92939 14057 0.010408 0.001284 13018 9282 UNB57752 7 623048 616327 112543 30257 0.007646 0.001052 28592 18649 UNB65032 7 341373 337408 93867 12458 0.009335 0.001258 11597 7602 UNB68414 7 903011 892782 127398 46817 0.004470 0.001007 45029 26863 UNB7514 7 4393289 4344149 238486 81157 0.006127 0.001105 78091 27787 UNB7601 7 168168 166109 60350 3860 0.014671 0.001283 3406 2615 USP14202 7 788510 779978 132520 44201 0.009601 0.001069 41897 23883 USP14838 7 611605 605342 121992 32351 0.009708 0.001095 30631 18480 USP1674 7 705562 698904 126482 38456 0.009741 0.001078 36574 23793 USP2902 7 500751 495534 93701 24389 0.006121 0.000979 23415 1059 USP4000 7 315176 311645 94176 11084 0.008306 0.001400 10338 6887 ## Alignment matrix statistics: snps matrix size: (24, 533446), 69.85% missing sites. sequence matrix size: (24, 10136148), 72.02% missing sites.