## 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 62012 filtered_by_rm_duplicates 2350 2350 59662 filtered_by_max_indels 731 731 58931 filtered_by_max_SNPs 250 210 58721 filtered_by_max_shared_het 242 159 58562 filtered_by_min_sample 48718 48718 9844 total_filtered_loci 52291 52168 9844 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage DGRP1 7601 DGRP4 1880 DGRP5 1964 DGRR1 7397 DGRR2 7258 DGRR7 2037 Dhy3Br 5853 Dhy8 7638 Dhym2 8083 Dhym3 8544 Dhym5 7862 Dma7Br 6597 DmaRef 6033 hybF1_1 5970 hybF1_2 5099 hybF1_3 7192 hybF1_4 6870 hybF1_5 5078 hybF1_6 7645 hybF1_7 7475 ## 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 1665 1665 11 1655 3320 12 1653 4973 13 1598 6571 14 1435 8006 15 1090 9096 16 571 9667 17 158 9825 18 14 9839 19 3 9842 20 2 9844 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 0 567 0 1485 0 1 947 947 1765 1765 2 1150 3247 1686 5137 3 1162 6733 1383 9286 4 1057 10961 1042 13454 5 948 15701 727 17089 6 834 20705 523 20227 7 666 25367 363 22768 8 551 29775 239 24680 9 397 33348 165 26165 10 326 36608 86 27025 11 236 39204 67 27762 12 175 41304 57 28446 13 140 43124 48 29070 14 109 44650 49 29756 15 95 46075 38 30326 16 76 47291 22 30678 17 64 48379 28 31154 18 55 49369 18 31478 19 54 50395 8 31630 20 39 51175 15 31930 21 32 51847 11 32161 22 44 52815 5 32271 23 25 53390 6 32409 24 18 53822 1 32433 25 18 54272 4 32533 26 21 54818 3 32611 27 16 55250 0 32611 28 17 55726 0 32611 29 5 55871 0 32611 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly DGRP1 7 1156523 1155942 125599 14995 0.017053 0.002739 14104 7601 DGRP4 7 2787142 2786919 107947 22564 0.020789 0.001768 21294 1880 DGRP5 7 2646077 2645859 164245 28315 0.023091 0.001864 26422 1964 DGRR1 7 1819325 1818946 200064 20549 0.022341 0.002772 18895 7397 DGRR2 7 1310554 1309710 78305 19594 0.014703 0.001346 19208 7258 DGRR7 7 3219581 3219235 190488 32994 0.025338 0.001764 30584 2037 Dhy3Br 7 4142222 4140701 155596 22653 0.024725 0.001980 21614 5853 Dhy8 7 2491284 2486503 301059 48565 0.029099 0.002928 45347 7638 Dhym2 7 988025 987640 123208 31034 0.021278 0.002609 29980 8083 Dhym3 7 1252793 1252296 120213 33962 0.020758 0.002326 32873 8544 Dhym5 7 1134658 1134005 231264 16486 0.018233 0.003297 15316 7862 Dma7Br 7 739708 739269 110047 19222 0.019189 0.003081 18310 6597 DmaRef 7 1088012 1087758 394562 19364 0.026989 0.005394 17383 6033 hybF1_1 7 1731936 1731234 94274 12817 0.017254 0.003862 12060 5970 hybF1_2 7 395359 395149 76254 8537 0.018469 0.003313 8047 5099 hybF1_3 7 1646277 1645803 123344 16390 0.018580 0.002426 15421 7192 hybF1_4 7 1400788 1400442 95853 14542 0.015613 0.002205 13970 6870 hybF1_5 7 659100 658899 81393 12203 0.014427 0.002935 11456 5078 hybF1_6 7 1631537 1631081 177538 18503 0.022482 0.002932 17023 7645 hybF1_7 7 1318224 1317726 142176 15203 0.017896 0.002865 14427 7475 ## Alignment matrix statistics: snps matrix size: (20, 55871), 37.71% missing sites. sequence matrix size: (20, 1388988), 37.41% missing sites.