## 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 3 filtered_by_rm_duplicates 0 0 3 filtered_by_max_indels 0 0 3 filtered_by_max_SNPs 0 0 3 filtered_by_max_shared_het 0 0 3 filtered_by_min_sample 3 3 0 total_filtered_loci 3 3 0 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage NBC-Cr-CL-01 0 NBC-Cr-CL-02 0 NBC-Cr-CL-03 0 NBC-Cr-CL-04 0 NBC-Cr-LM3-03 0 NBC-Cr-LM3-04 0 NBC-Cr-LM3-07 0 SBR-Cr-ABI-01 0 SBR-Cr-ABI-02 0 SBR-Cr-ABI-03 0 SBR-Cr-ABI-04 0 SBR-Cr-BP-03 0 SBR-Cr-BP-07 0 SBR-Cr-BT-01 0 SCM-Cr-IF-01 0 SCM-Cr-JR3-01 0 SCM-Cr-JR3-02 0 SCM-Cr-JR3-05 0 SCM-Cr-JR3-08 0 ## 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 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 0 0 0 0 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly NBC-Cr-CL-01 7 1295 1283 795 6 0.014309 0.004773 5 0 NBC-Cr-CL-02 7 1373 1365 841 9 0.027466 0.003056 7 0 NBC-Cr-CL-03 7 1209 1204 760 6 0.020690 0.000002 4 0 NBC-Cr-CL-04 7 1045 1040 659 7 0.014545 0.001663 6 0 NBC-Cr-LM3-03 7 1438 1424 861 5 0.000031 0.008736 4 0 NBC-Cr-LM3-04 7 741 733 499 2 0.017598 0.000739 2 0 NBC-Cr-LM3-07 7 1284 1272 790 2 0.072445 0.010040 1 0 SBR-Cr-ABI-01 7 1009 1007 638 3 0.017273 0.003502 2 0 SBR-Cr-ABI-02 7 1250 1238 769 4 0.000016 0.001215 4 0 SBR-Cr-ABI-03 7 1274 1264 825 5 0.016776 0.001680 4 0 SBR-Cr-ABI-04 7 727 722 478 3 0.000729 0.003599 2 0 SBR-Cr-BP-03 7 797 794 520 2 0.002847 0.006910 1 0 SBR-Cr-BP-07 7 1545 1524 917 10 0.011195 0.000882 9 0 SBR-Cr-BT-01 7 1415 1403 849 6 0.012680 0.000829 5 0 SCM-Cr-IF-01 7 372 370 239 3 0.036845 0.010472 1 0 SCM-Cr-JR3-01 7 1181 1173 747 5 0.016892 0.001163 4 0 SCM-Cr-JR3-02 7 1141 1140 717 1 0.000078 0.002080 1 0 SCM-Cr-JR3-05 7 574 571 381 2 0.057649 0.004404 1 0 SCM-Cr-JR3-08 7 803 797 520 3 0.049391 0.001216 1 0 ## Alignment matrix statistics: