## 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 91099 filtered_by_rm_duplicates 711 711 90388 filtered_by_max_indels 7626 7626 82762 filtered_by_max_SNPs 33 1 82761 filtered_by_max_shared_het 718 555 82206 filtered_by_min_sample 53660 53660 28546 total_filtered_loci 62748 62553 28546 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage T_12 24 T_13 14826 T_14 8639 T_15 12844 T_16 14175 T_17 3907 T_18 6260 T_19 171 T_20 3214 T_21 11506 T_22 7 T_23 19827 T_24 13255 T_fronteriensis_2203029 15729 T_fronteriensis_2203030 16349 T_halli_2110027 19550 T_halli_2110028 16735 T_halli_2110029 10355 T_pefauri_2209002 2596 T_pefauri_2209003 11021 T_pefauri_2209004 8926 T_philippii_2203042 20708 T_philippii_2203043 16822 T_philippii_2203044 28 ## 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 5611 5611 5 3695 9306 6 3031 12337 7 2592 14929 8 1995 16924 9 2435 19359 10 1266 20625 11 1087 21712 12 906 22618 13 749 23367 14 718 24085 15 834 24919 16 873 25792 17 767 26559 18 760 27319 19 706 28025 20 480 28505 21 41 28546 22 0 28546 23 0 28546 24 0 28546 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 8530 0 11971 0 1 3826 3826 3495 3495 2 3383 10592 3132 9759 3 3290 20462 2794 18141 4 2594 30838 2124 26637 5 1942 40548 1514 34207 6 1416 49044 1134 41011 7 978 55890 707 45960 8 714 61602 524 50152 9 492 66030 330 53122 10 332 69350 214 55262 11 217 71737 125 56637 12 170 73777 108 57933 13 134 75519 82 58999 14 90 76779 54 59755 15 61 77694 37 60310 16 63 78702 33 60838 17 39 79365 23 61229 18 29 79887 21 61607 19 29 80438 13 61854 20 23 80898 21 62274 21 28 81486 17 62631 22 16 81838 11 62873 23 17 82229 6 63011 24 12 82517 7 63179 25 6 82667 0 63179 26 9 82901 6 63335 27 5 83036 4 63443 28 8 83260 6 63611 29 11 83579 2 63669 30 5 83729 6 63849 31 5 83884 1 63880 32 5 84044 6 64072 33 12 84440 4 64204 34 8 84712 0 64204 35 6 84922 2 64274 36 5 85102 4 64418 37 4 85250 0 64418 38 4 85402 4 64570 39 5 85597 1 64609 40 6 85837 1 64649 41 3 85960 1 64690 42 3 86086 0 64690 43 4 86258 1 64733 44 1 86302 0 64733 45 1 86347 0 64733 46 0 86347 0 64733 47 0 86347 0 64733 48 1 86395 0 64733 49 1 86444 0 64733 50 1 86494 0 64733 51 0 86494 0 64733 52 0 86494 0 64733 53 0 86494 0 64733 54 1 86548 0 64733 55 1 86603 0 64733 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly T_12 7 4692328 4611733 164738 41413 0.008978 0.001688 37823 24 T_13 7 1837573 1812816 110732 24515 0.003070 0.001165 23541 14826 T_14 7 417377 411372 48926 12381 0.003543 0.001592 11852 8639 T_15 7 932452 920578 72316 18775 0.003181 0.001300 18034 12844 T_16 7 1018614 1005916 73641 21081 0.002958 0.001126 20353 14175 T_17 7 200418 197903 33540 6066 0.005304 0.001899 5624 3907 T_18 7 288310 283939 41423 9205 0.003912 0.001474 8740 6260 T_19 7 25236 24877 9435 373 0.013731 0.003384 292 171 T_20 7 175391 172840 31674 5648 0.005347 0.001880 5255 3214 T_21 7 1014325 1000920 67784 19473 0.003646 0.001296 18557 11506 T_22 7 415773 408698 49601 10732 0.013074 0.004086 9308 7 T_23 7 10758498 10611586 330203 46329 0.006469 0.000746 42927 19827 T_24 7 852549 841800 64254 19260 0.003097 0.001158 18604 13255 T_fronteriensis_2203029 7 1424893 1405064 81794 24358 0.003714 0.001278 23359 15729 T_fronteriensis_2203030 7 1593824 1573551 82149 25483 0.002992 0.001110 24514 16349 T_halli_2110027 7 3035990 2999843 111892 35914 0.002586 0.001002 34718 19550 T_halli_2110028 7 1615955 1594830 81770 26231 0.003068 0.001011 25332 16735 T_halli_2110029 7 574281 567354 62825 14926 0.003351 0.001457 14301 10355 T_pefauri_2209002 7 129226 127481 29490 4408 0.006110 0.002349 4058 2596 T_pefauri_2209003 7 957069 946523 67624 19650 0.003919 0.001157 18806 11021 T_pefauri_2209004 7 547087 540852 54065 15629 0.004611 0.001260 14937 8926 T_philippii_2203042 7 6643490 6554492 191662 48857 0.002863 0.000953 46784 20708 T_philippii_2203043 7 1641062 1617657 93906 26755 0.003193 0.001113 25766 16822 T_philippii_2203044 7 6210569 6108180 198858 47281 0.008752 0.001329 43265 28 ## Alignment matrix statistics: snps matrix size: (24, 86603), 57.92% missing sites. sequence matrix size: (24, 8026992), 63.83% missing sites.