## The number of loci caught by each filter. ## ipyrad API location: [assembly].statsfiles.s7_filters total_filters applied_order retained_loci total_prefiltered_loci 237172 0 237172 filtered_by_rm_duplicates 48311 48311 188861 filtered_by_max_indels 0 0 188861 filtered_by_max_snps 0 0 188861 filtered_by_max_shared_het 0 0 188861 filtered_by_min_sample 0 0 188861 filtered_by_max_alleles 2171 715 188146 total_filtered_loci 188146 0 188146 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage Cmac-15-10-1-R_S18001_PairedTrim 188146 Cmac-15-10-10-R_S17001_PairedTrim 188146 Cmac-15-10-2-R_S19001_PairedTrim 188146 Cmac-15-10-3-R_S20001_PairedTrim 188146 Cmac-15-10-4-R_S21001_PairedTrim 188146 Cmac-15-10-5-R_S22001_PairedTrim 188146 Cmac-15-10-6-R_S23001_PairedTrim 188146 Cmac-15-10-7-R_S24001_PairedTrim 188146 Cmac-15-10-8-R_S25001_PairedTrim 188146 Cmac-15-10-9-R_S26001_PairedTrim 188146 Cmac-15-11-1-R_S28001_PairedTrim 188146 Cmac-15-11-10-R_S27001_PairedTrim 188146 Cmac-15-11-2-R_S29001_PairedTrim 188146 Cmac-15-11-3-R_S30001_PairedTrim 188146 Cmac-15-11-4-R_S31001_PairedTrim 188146 Cmac-15-11-5-R_S32001_PairedTrim 188146 Cmac-15-11-6-R_S33001_PairedTrim 188146 Cmac-15-11-7-R_S34001_PairedTrim 188146 Cmac-15-11-8-R_S35001_PairedTrim 188146 Cmac-15-11-9-R_S36001_PairedTrim 188146 Cmac-15-12-1-R_S38001_PairedTrim 188146 Cmac-15-12-10-R_S37001_PairedTrim 188146 Cmac-15-12-2-R_S39001_PairedTrim 188146 Cmac-15-12-3-R_S40001_PairedTrim 188146 Cmac-15-12-4-R_S41001_PairedTrim 188146 Cmac-15-12-5-R_S42001_PairedTrim 188146 Cmac-15-12-6-R_S43001_PairedTrim 188146 Cmac-15-12-7-R_S44001_PairedTrim 188146 Cmac-15-12-8-R_S45001_PairedTrim 188146 Cmac-15-12-9-R_S46001_PairedTrim 188146 Cmac-15-3-1-R_S47001_PairedTrim 188146 Cmac-15-3-2-R_S48001_PairedTrim 188146 Cmac-15-3-3-R_S49001_PairedTrim 188146 Cmac-15-3-4-R_S50001_PairedTrim 188146 Cmac-15-3-5-R_S51001_PairedTrim 188146 Cmac-15-3-6-R_S52001_PairedTrim 188146 Cmac-15-3-7-R_S53001_PairedTrim 188146 Cmac-15-4-1-R_S55001_PairedTrim 188146 Cmac-15-4-10-R_S54001_PairedTrim 188146 Cmac-15-4-2-R_S56001_PairedTrim 188146 Cmac-15-4-3-R_S57001_PairedTrim 188146 Cmac-15-4-4-R_S58001_PairedTrim 188146 Cmac-15-4-5-R_S59001_PairedTrim 188146 Cmac-15-4-6-R_S60001_PairedTrim 188146 Cmac-15-4-7-R_S61001_PairedTrim 188146 Cmac-15-4-8-z_S93001_PairedTrim 188146 Cmac-15-4-9-R_S63001_PairedTrim 188146 Cmac-15-5-1-R_S65001_PairedTrim 188146 Cmac-15-5-10-R_S64001_PairedTrim 188146 Cmac-15-5-2-R_S66001_PairedTrim 188146 Cmac-15-5-3-R_S67001_PairedTrim 188146 Cmac-15-5-4-R_S68001_PairedTrim 188146 Cmac-15-5-5-R_S69001_PairedTrim 188146 Cmac-15-5-6-R_S70001_PairedTrim 188146 Cmac-15-5-8-R_S72001_PairedTrim 188146 Cmac-15-5-9-R_S73001_PairedTrim 188146 Cmac-15-66-R_S74001_PairedTrim 188146 Cmac-15-67-R_S75001_PairedTrim 188146 Cmac-15-68-R_S76001_PairedTrim 188146 Cmac-15-8-1-R_S78001_PairedTrim 188146 Cmac-15-8-10-R_S77001_PairedTrim 188146 Cmac-15-8-2-R_S79001_PairedTrim 188146 Cmac-15-8-3-R_S80001_PairedTrim 188146 Cmac-15-8-4-R_S81001_PairedTrim 188146 Cmac-15-8-5-R_S82001_PairedTrim 188146 Cmac-15-8-6-R_S83001_PairedTrim 188146 Cmac-15-8-7-R_S84001_PairedTrim 188146 Cmac-15-8-8-R_S85001_PairedTrim 188146 Cmac-15-8-9-R_S86001_PairedTrim 188146 Cmac-15-9-1-R_S88001_PairedTrim 188146 Cmac-15-9-10-R_S87001_PairedTrim 188146 Cmac-15-9-2-R_S89001_PairedTrim 188146 Cmac-15-9-3-R_S90001_PairedTrim 188146 Cmac-15-9-4-R_S91001_PairedTrim 188146 Cmac-15-9-5-R_S92001_PairedTrim 188146 Cmac-15-9-6-R_S93001_PairedTrim 188146 Cmac-15-9-7-R_S94001_PairedTrim 188146 Cmac-15-9-8-R_S95001_PairedTrim 188146 Cmac-15-9-9-R_S96001_PairedTrim 188146 Cml-15-79-z_S95001_PairedTrim 188146 Cmv-15-80-z_S96001_PairedTrim 188146 ## 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 0 0 7 0 0 8 0 0 9 0 0 10 0 0 11 0 0 12 0 0 13 0 0 14 0 0 15 0 0 16 0 0 17 0 0 18 0 0 19 0 0 20 0 0 21 0 0 22 0 0 23 0 0 24 0 0 25 0 0 26 0 0 27 0 0 28 0 0 29 0 0 30 0 0 31 0 0 32 0 0 33 0 0 34 0 0 35 0 0 36 0 0 37 0 0 38 0 0 39 0 0 40 0 0 41 0 0 42 0 0 43 0 0 44 0 0 45 0 0 46 0 0 47 0 0 48 0 0 49 0 0 50 0 0 51 0 0 52 0 0 53 0 0 54 0 0 55 0 0 56 0 0 57 0 0 58 0 0 59 0 0 60 0 0 61 0 0 62 0 0 63 0 0 64 0 0 65 0 0 66 0 0 67 0 0 68 0 0 69 0 0 70 0 0 71 0 0 72 0 0 73 0 0 74 0 0 75 0 0 76 0 0 77 0 0 78 0 0 79 0 0 80 0 0 81 188146 188146 ## 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 188146 0 188146 0 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly Cmac-15-10-1-R_S18001_PairedTrim 7 3226059 3226059 1710460 69748 0.099794 0.042248 40184 188146 Cmac-15-10-10-R_S17001_PairedTrim 7 3061231 3061231 1646596 65111 0.099723 0.041050 37659 188146 Cmac-15-10-2-R_S19001_PairedTrim 7 3546099 3546098 1823912 77834 0.123702 0.037125 45248 188146 Cmac-15-10-3-R_S20001_PairedTrim 7 2823772 2823772 1552845 58095 0.105314 0.039770 33853 188146 Cmac-15-10-4-R_S21001_PairedTrim 7 2952432 2952432 1587620 62444 0.096075 0.041472 36436 188146 Cmac-15-10-5-R_S22001_PairedTrim 7 4366494 4366493 2142230 107204 0.123133 0.040112 60205 188146 Cmac-15-10-6-R_S23001_PairedTrim 7 1964115 1964115 1134556 38354 0.105314 0.039770 22166 188146 Cmac-15-10-7-R_S24001_PairedTrim 7 3150132 3150132 1662735 68429 0.096075 0.041472 39850 188146 Cmac-15-10-8-R_S25001_PairedTrim 7 3428057 3428056 1788610 75185 0.099794 0.042248 43576 188146 Cmac-15-10-9-R_S26001_PairedTrim 7 2989707 2989707 1601274 63892 0.099794 0.042248 37020 188146 Cmac-15-11-1-R_S28001_PairedTrim 7 2994624 2994623 1626303 62317 0.096075 0.041472 36204 188146 Cmac-15-11-10-R_S27001_PairedTrim 7 2766663 2766663 1496505 58415 0.103226 0.037990 34039 188146 Cmac-15-11-2-R_S29001_PairedTrim 7 3149898 3149898 1681795 67977 0.099794 0.042248 39286 188146 Cmac-15-11-3-R_S30001_PairedTrim 7 2325352 2325352 1316340 46071 0.105334 0.036034 26935 188146 Cmac-15-11-4-R_S31001_PairedTrim 7 2739860 2739860 1508868 56425 0.105314 0.039770 33016 188146 Cmac-15-11-5-R_S32001_PairedTrim 7 3250529 3250529 1720865 69363 0.093139 0.041424 40584 188146 Cmac-15-11-6-R_S33001_PairedTrim 7 2214942 2214942 1243648 44979 0.123702 0.037125 26100 188146 Cmac-15-11-7-R_S34001_PairedTrim 7 2359901 2359901 1318122 48025 0.123702 0.037125 28155 188146 Cmac-15-11-8-R_S35001_PairedTrim 7 2797253 2797253 1508635 58121 0.118197 0.035395 34027 188146 Cmac-15-11-9-R_S36001_PairedTrim 7 2939061 2939061 1574291 61870 0.090143 0.039249 36129 188146 Cmac-15-12-1-R_S38001_PairedTrim 7 2735464 2735464 1518849 56521 0.104112 0.041858 32530 188146 Cmac-15-12-10-R_S37001_PairedTrim 7 2313218 2313218 1312924 46204 0.109991 0.037848 26940 188146 Cmac-15-12-2-R_S39001_PairedTrim 7 2731852 2731852 1478838 55929 0.096806 0.034713 32601 188146 Cmac-15-12-3-R_S40001_PairedTrim 7 2885533 2885532 1551556 61151 0.096304 0.037647 35406 188146 Cmac-15-12-4-R_S41001_PairedTrim 7 3235654 3235654 1717015 69747 0.099794 0.042248 40271 188146 Cmac-15-12-5-R_S42001_PairedTrim 7 2574953 2574953 1418904 53037 0.105314 0.039770 30794 188146 Cmac-15-12-6-R_S43001_PairedTrim 7 3238047 3238047 1709475 70136 0.088478 0.039909 41008 188146 Cmac-15-12-7-R_S44001_PairedTrim 7 3270119 3270119 1695007 69575 0.119059 0.036844 40596 188146 Cmac-15-12-8-R_S45001_PairedTrim 7 3225803 3225802 1677261 69315 0.093139 0.041424 40073 188146 Cmac-15-12-9-R_S46001_PairedTrim 7 2218085 2218085 1256794 44181 0.093139 0.041424 25800 188146 Cmac-15-3-1-R_S47001_PairedTrim 7 2242195 2242195 1281311 44570 0.127786 0.038777 25941 188146 Cmac-15-3-2-R_S48001_PairedTrim 7 2213990 2213990 1350379 43581 0.109336 0.037018 26532 188146 Cmac-15-3-3-R_S49001_PairedTrim 7 2581088 2581088 1403135 53176 0.118197 0.035395 30813 188146 Cmac-15-3-4-R_S50001_PairedTrim 7 2669544 2669544 1449188 54823 0.120405 0.034474 31950 188146 Cmac-15-3-5-R_S51001_PairedTrim 7 2571329 2571329 1404380 52836 0.118197 0.035395 30689 188146 Cmac-15-3-6-R_S52001_PairedTrim 7 2851154 2851154 1582924 59890 0.108430 0.041468 34633 188146 Cmac-15-3-7-R_S53001_PairedTrim 7 2666568 2666568 1463608 55159 0.100204 0.039344 32078 188146 Cmac-15-4-1-R_S55001_PairedTrim 7 2434855 2434855 1341205 49663 0.114049 0.036432 28888 188146 Cmac-15-4-10-R_S54001_PairedTrim 7 2478962 2478962 1372882 50363 0.090143 0.039249 29299 188146 Cmac-15-4-2-R_S56001_PairedTrim 7 2211133 2211133 1227502 45034 0.093139 0.041424 26161 188146 Cmac-15-4-3-R_S57001_PairedTrim 7 2316509 2316509 1347470 45475 0.099794 0.042248 26499 188146 Cmac-15-4-4-R_S58001_PairedTrim 7 2963444 2963443 1629754 62200 0.104112 0.041858 35952 188146 Cmac-15-4-5-R_S59001_PairedTrim 7 2141634 2141634 1204179 41861 0.119059 0.036844 24575 188146 Cmac-15-4-6-R_S60001_PairedTrim 7 2256429 2256428 1291177 44205 0.105334 0.036034 25751 188146 Cmac-15-4-7-R_S61001_PairedTrim 7 3029957 3029956 1624512 64111 0.105314 0.039770 37193 188146 Cmac-15-4-8-z_S93001_PairedTrim 7 1801470 1801470 1122531 33812 0.116555 0.037678 19734 188146 Cmac-15-4-9-R_S63001_PairedTrim 7 2620835 2620835 1440942 52917 0.118197 0.035395 30835 188146 Cmac-15-5-1-R_S65001_PairedTrim 7 2292626 2292626 1281347 46108 0.088478 0.039909 27113 188146 Cmac-15-5-10-R_S64001_PairedTrim 7 3311357 3311357 1887864 70694 0.113710 0.043215 40400 188146 Cmac-15-5-2-R_S66001_PairedTrim 7 3055226 3055226 1639696 64656 0.103226 0.037990 37439 188146 Cmac-15-5-3-R_S67001_PairedTrim 7 2398850 2398850 1415723 46603 0.117059 0.040203 26982 188146 Cmac-15-5-4-R_S68001_PairedTrim 7 2219826 2219826 1269111 43772 0.096059 0.040501 25593 188146 Cmac-15-5-5-R_S69001_PairedTrim 7 3523302 3523302 1834448 78369 0.108430 0.041468 45017 188146 Cmac-15-5-6-R_S70001_PairedTrim 7 2769186 2769186 1512572 58231 0.099723 0.041050 33918 188146 Cmac-15-5-8-R_S72001_PairedTrim 7 2536316 2536316 1390019 53099 0.105314 0.039770 30712 188146 Cmac-15-5-9-R_S73001_PairedTrim 7 2383885 2383885 1342367 47944 0.103226 0.037990 27997 188146 Cmac-15-66-R_S74001_PairedTrim 7 2506356 2506355 1391581 51763 0.103226 0.037990 29582 188146 Cmac-15-67-R_S75001_PairedTrim 7 2504342 2504342 1412694 51096 0.116555 0.037678 29581 188146 Cmac-15-68-R_S76001_PairedTrim 7 2808167 2808164 1520178 58137 0.120405 0.034474 33920 188146 Cmac-15-8-1-R_S78001_PairedTrim 7 2828073 2828073 1538765 59418 0.103226 0.037990 34586 188146 Cmac-15-8-10-R_S77001_PairedTrim 7 3387349 3387349 1796605 72917 0.099794 0.042248 42121 188146 Cmac-15-8-2-R_S79001_PairedTrim 7 3067845 3067845 1646855 65588 0.108449 0.036216 37997 188146 Cmac-15-8-3-R_S80001_PairedTrim 7 3684010 3684010 1912403 83339 0.108430 0.041468 47785 188146 Cmac-15-8-4-R_S81001_PairedTrim 7 2615803 2615803 1421720 54749 0.096059 0.040501 31425 188146 Cmac-15-8-5-R_S82001_PairedTrim 7 2639260 2639260 1441010 54861 0.123702 0.037125 31962 188146 Cmac-15-8-6-R_S83001_PairedTrim 7 4568539 4568539 2224595 106027 0.103226 0.037990 61986 188146 Cmac-15-8-7-R_S84001_PairedTrim 7 3155249 3155249 1681505 67467 0.103226 0.037990 39532 188146 Cmac-15-8-8-R_S85001_PairedTrim 7 2545502 2545502 1393579 52739 0.093139 0.041424 30703 188146 Cmac-15-8-9-R_S86001_PairedTrim 7 2866091 2866091 1565600 59239 0.093139 0.041424 34470 188146 Cmac-15-9-1-R_S88001_PairedTrim 7 3510180 3510180 1808858 77207 0.123702 0.037125 45159 188146 Cmac-15-9-10-R_S87001_PairedTrim 7 2890594 2890594 1574987 61356 0.099794 0.042248 35564 188146 Cmac-15-9-2-R_S89001_PairedTrim 7 2065394 2065393 1166358 42034 0.103226 0.037990 24452 188146 Cmac-15-9-3-R_S90001_PairedTrim 7 2759737 2759737 1492072 56904 0.093139 0.041424 33159 188146 Cmac-15-9-4-R_S91001_PairedTrim 7 2766577 2766577 1504948 58656 0.100204 0.039344 34007 188146 Cmac-15-9-5-R_S92001_PairedTrim 7 2406622 2406622 1368095 49134 0.108430 0.041468 28513 188146 Cmac-15-9-6-R_S93001_PairedTrim 7 2657575 2657575 1480767 55374 0.114979 0.038909 31831 188146 Cmac-15-9-7-R_S94001_PairedTrim 7 3041203 3041202 1648565 65397 0.116555 0.037678 37315 188146 Cmac-15-9-8-R_S95001_PairedTrim 7 3008307 3008307 1645193 62972 0.108449 0.036216 36164 188146 Cmac-15-9-9-R_S96001_PairedTrim 7 3420482 3420482 1824475 74035 0.099794 0.042248 42950 188146 Cml-15-79-z_S95001_PairedTrim 7 1481951 1481951 956491 26684 0.110369 0.040367 15696 188146 Cmv-15-80-z_S96001_PairedTrim 7 1841175 1841175 1164733 35173 0.113710 0.043215 20574 188146