## The number of loci caught by each filter. ## ipyrad API location: [assembly].statsfiles.s7_filters total_filters applied_order retained_loci total_prefiltered_loci 41449 0 41449 filtered_by_rm_duplicates 3644 3644 37805 filtered_by_max_indels 5333 2882 34923 filtered_by_max_snps 4342 1131 33792 filtered_by_max_shared_het 1070 449 33343 filtered_by_min_sample 15908 15773 17570 filtered_by_max_alleles 12143 6470 11100 total_filtered_loci 11100 0 11100 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage Carm-15-1-1-z_S42_001_PairedTrim 810 Carm-15-1-10-z_S41_001_PairedTrim 859 Carm-15-1-2-z_S43_001_PairedTrim 930 Carm-15-1-3-z_S44_001_PairedTrim 1060 Carm-15-1-4-z_S45_001_PairedTrim 825 Carm-15-1-5-z_S46_001_PairedTrim 786 Carm-15-1-6-z_S47_001_PairedTrim 965 Carm-15-1-7-z_S48_001_PairedTrim 928 Carm-15-1-8-z_S49_001_PairedTrim 1056 Carm-15-1-9-z_S50_001_PairedTrim 990 Carm-15-13-1-z_S2_001_PairedTrim 1085 Carm-15-13-10-z_S1_001_PairedTrim 1081 Carm-15-13-2-z_S3_001_PairedTrim 2145 Carm-15-13-3-z_S4_001_PairedTrim 1156 Carm-15-13-4-z_S5_001_PairedTrim 1026 Carm-15-13-5-z_S6_001_PairedTrim 1317 Carm-15-13-6-z_S7_001_PairedTrim 749 Carm-15-13-7-z_S8_001_PairedTrim 1141 Carm-15-13-8-z_S9_001_PairedTrim 1458 Carm-15-13-9-z_S10_001_PairedTrim 1060 Carm-15-14-1-z_S12_001_PairedTrim 1937 Carm-15-14-10-z_S11_001_PairedTrim 1083 Carm-15-14-2-z_S13_001_PairedTrim 1188 Carm-15-14-3-z_S14_001_PairedTrim 1148 Carm-15-14-4-z_S15_001_PairedTrim 946 Carm-15-14-5-z_S16_001_PairedTrim 1476 Carm-15-14-6-z_S17_001_PairedTrim 1116 Carm-15-14-7-z_S18_001_PairedTrim 1237 Carm-15-14-8-z_S19_001_PairedTrim 1488 Carm-15-14-9-z_S20_001_PairedTrim 1212 Carm-15-15-1-z_S22_001_PairedTrim 1414 Carm-15-15-10-z_S21_001_PairedTrim 821 Carm-15-15-2-z_S23_001_PairedTrim 1306 Carm-15-15-3-z_S24_001_PairedTrim 1027 Carm-15-15-4-z_S25_001_PairedTrim 1308 Carm-15-15-5-z_S26_001_PairedTrim 2020 Carm-15-15-6-z_S27_001_PairedTrim 2264 Carm-15-15-7-z_S28_001_PairedTrim 1144 Carm-15-15-8-z_S29_001_PairedTrim 891 Carm-15-15-9-z_S30_001_PairedTrim 1281 Carm-15-16-1-z_S32_001_PairedTrim 1031 Carm-15-16-10-z_S31_001_PairedTrim 1298 Carm-15-16-2-z_S33_001_PairedTrim 981 Carm-15-16-3-z_S34_001_PairedTrim 1028 Carm-15-16-4-z_S35_001_PairedTrim 1161 Carm-15-16-5-z_S36_001_PairedTrim 1028 Carm-15-16-6-z_S37_001_PairedTrim 892 Carm-15-16-7-z_S38_001_PairedTrim 1526 Carm-15-16-8-z_S39_001_PairedTrim 1352 Carm-15-16-9-z_S40_001_PairedTrim 637 Carm-15-2-1-z_S71_001_PairedTrim 1025 Carm-15-2-10-z_S70_001_PairedTrim 902 Carm-15-2-2-z_S72_001_PairedTrim 739 Carm-15-2-3-z_S73_001_PairedTrim 909 Carm-15-2-4-z_S74_001_PairedTrim 923 Carm-15-2-5-z_S75_001_PairedTrim 646 Carm-15-2-6-z_S76_001_PairedTrim 486 Carm-15-2-7-z_S77_001_PairedTrim 1198 Carm-15-2-8-z_S78_001_PairedTrim 924 Carm-15-2-9-z_S79_001_PairedTrim 2286 Carm-15-20-1-z_S52_001_PairedTrim 1047 Carm-15-20-10-z_S51_001_PairedTrim 884 Carm-15-20-2-z_S53_001_PairedTrim 763 Carm-15-20-3-z_S54_001_PairedTrim 1563 Carm-15-20-4-z_S55_001_PairedTrim 990 Carm-15-20-5-z_S56_001_PairedTrim 1264 Carm-15-20-6-z_S57_001_PairedTrim 960 Carm-15-20-7-z_S58_001_PairedTrim 1089 Carm-15-20-9-z_S60_001_PairedTrim 1261 Carm-15-24-1-z_S62_001_PairedTrim 943 Carm-15-24-10-z_S61_001_PairedTrim 1452 Carm-15-24-2-z_S63_001_PairedTrim 908 Carm-15-24-3-z_S64_001_PairedTrim 903 Carm-15-24-4-z_S65_001_PairedTrim 838 Carm-15-24-5-z_S66_001_PairedTrim 823 Carm-15-24-6-z_S67_001_PairedTrim 1991 Carm-15-24-7-z_S68_001_PairedTrim 1025 Carm-15-24-8-z_S69_001_PairedTrim 752 Carm-15-24-9-R_S11_001_PairedTrim 1758 Carm-15-48_S2_001_PairedTrim 1476 Carm-15-49_S3_001_PairedTrim 1476 Carm-15-51_S4_001_PairedTrim 1272 Carm-15-52_S5_001_PairedTrim 1397 Carm-15-53_S6_001_PairedTrim 1645 Carm-15-54_S7_001_PairedTrim 1623 Carm-15-56_S8_001_PairedTrim 1146 Carm-15-57_S9_001_PairedTrim 1427 Carm-15-58_S10_001_PairedTrim 1440 Carm-15-6-1-z_S81_001_PairedTrim 1090 Carm-15-6-10-z_S80_001_PairedTrim 1258 Carm-15-6-2-z_S82_001_PairedTrim 919 Carm-15-6-3-z_S83_001_PairedTrim 1235 Carm-15-6-4-z_S84_001_PairedTrim 685 Carm-15-6-5-z_S85_001_PairedTrim 1186 Carm-15-6-6-z_S86_001_PairedTrim 999 Carm-15-6-8-z_S88_001_PairedTrim 573 Carm-15-6-9-z_S89_001_PairedTrim 1131 Carm-15-61-R_S13_001_PairedTrim 1984 Carm-15-62_S11_001_PairedTrim 1558 Carm-15-71-z_S90_001_PairedTrim 872 Carm-15-72-z_S91_001_PairedTrim 1187 Carms-15-50_S12_001_PairedTrim 1764 Crms-15-55_S87_001_PairedTrim 1719 ## 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 2838 2838 5 1823 4661 6 1277 5938 7 854 6792 8 685 7477 9 500 7977 10 386 8363 11 332 8695 12 254 8949 13 232 9181 14 169 9350 15 143 9493 16 127 9620 17 112 9732 18 98 9830 19 72 9902 20 80 9982 21 63 10045 22 52 10097 23 51 10148 24 45 10193 25 36 10229 26 37 10266 27 48 10314 28 32 10346 29 30 10376 30 37 10413 31 22 10435 32 29 10464 33 23 10487 34 18 10505 35 26 10531 36 19 10550 37 18 10568 38 26 10594 39 15 10609 40 11 10620 41 17 10637 42 18 10655 43 15 10670 44 18 10688 45 13 10701 46 10 10711 47 13 10724 48 15 10739 49 17 10756 50 17 10773 51 13 10786 52 11 10797 53 10 10807 54 9 10816 55 10 10826 56 8 10834 57 10 10844 58 8 10852 59 6 10858 60 10 10868 61 5 10873 62 5 10878 63 6 10884 64 5 10889 65 7 10896 66 6 10902 67 7 10909 68 0 10909 69 5 10914 70 3 10917 71 5 10922 72 2 10924 73 5 10929 74 1 10930 75 3 10933 76 6 10939 77 5 10944 78 5 10949 79 4 10953 80 1 10954 81 4 10958 82 3 10961 83 6 10967 84 6 10973 85 2 10975 86 3 10978 87 3 10981 88 4 10985 89 1 10986 90 4 10990 91 2 10992 92 4 10996 93 4 11000 94 2 11002 95 2 11004 96 5 11009 97 10 11019 98 9 11028 99 8 11036 100 20 11056 101 17 11073 102 16 11089 103 11 11100 ## The distribution of SNPs (var and pis) across loci. ## var = all variable sites (pis + autapomorphies) ## pis = parsimony informative site (minor allele in >1 sample) ## ipyrad API location: [assembly].stats_dfs.s7_snps var sum_var pis sum_pis 0 990 0 1736 0 1 418 418 695 695 2 331 1080 522 1739 3 266 1878 418 2993 4 238 2830 399 4589 5 200 3830 378 6479 6 227 5192 351 8585 7 181 6459 359 11098 8 166 7787 340 13818 9 192 9515 330 16788 10 197 11485 312 19908 11 205 13740 273 22911 12 199 16128 252 25935 13 200 18728 258 29289 14 206 21612 288 33321 15 203 24657 235 36846 16 231 28353 210 40206 17 223 32144 218 43912 18 206 35852 195 47422 19 217 39975 199 51203 20 228 44535 151 54223 21 198 48693 187 58150 22 256 54325 176 62022 23 204 59017 147 65403 24 208 64009 148 68955 25 205 69134 144 72555 26 190 74074 126 75831 27 205 79609 118 79017 28 196 85097 113 82181 29 206 91071 119 85632 30 184 96591 108 88872 31 179 102140 93 91755 32 174 107708 93 94731 33 142 112394 80 97371 34 167 118072 72 99819 35 158 123602 83 102724 36 163 129470 74 105388 37 152 135094 69 107941 38 154 140946 70 110601 39 123 145743 77 113604 40 137 151223 72 116484 41 90 154913 68 119272 42 77 158147 45 121162 43 89 161974 50 123312 44 71 165098 63 126084 45 84 168878 57 128649 46 81 172604 62 131501 47 98 177210 45 133616 48 80 181050 56 136304 49 79 184921 38 138166 50 73 188571 32 139766 51 74 192345 48 142214 52 81 196557 47 144658 53 95 201592 41 146831 54 76 205696 26 148235 55 69 209491 26 149665 56 71 213467 23 150953 57 52 216431 17 151922 58 65 220201 12 152618 59 61 223800 14 153444 60 62 227520 9 153984 61 52 230692 10 154594 62 47 233606 6 154966 63 42 236252 9 155533 64 55 239772 5 155853 65 40 242372 1 155918 66 31 244418 1 155984 67 40 247098 1 156051 68 29 249070 0 156051 69 19 250381 0 156051 70 19 251711 0 156051 71 18 252989 0 156051 72 16 254141 0 156051 73 14 255163 0 156051 74 7 255681 0 156051 75 5 256056 0 156051 76 3 256284 0 156051 77 3 256515 0 156051 78 4 256827 0 156051 79 1 256906 0 156051 80 2 257066 0 156051