## 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 15401 filtered_by_rm_duplicates 116 116 15285 filtered_by_max_indels 658 658 14627 filtered_by_max_SNPs 0 0 14627 filtered_by_max_shared_het 69 62 14565 filtered_by_min_sample 12673 12673 1892 total_filtered_loci 13516 13509 1892 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage EC01_US_AZVV_Fo_perp 394 EC04_US_AZVV_Po_mar_occ 299 EC05_US_AZMG_Fo_gnav 191 EC07_MX_SOSJSD_Ph_rhea 76 EC107_US_AZCBP_La_sp 1181 EC111_US_AZCP_Cr_C 1174 EC113_US_AZCP_Cr_C 390 EC114_US_AZCP_Li_apic 1168 EC11_MX_SOSE_Fo_gnav 21 EC15_MX_SOSJRZ_Ph_rhea 55 EC16_MX_SOSE_Ph_obtu 25 EC18_US_AZPC_Ph_obtu 151 EC19_US_AZPC_Tr_ariz 292 EC20_MX_SOSJRSF_Ph_rhea 266 EC21_MX_SOSJRZ_La_sp 151 EC24_US_AZCH_Cr_C 829 EC33_US_AZPAY_Li_apic 311 EC35_US_AZPAY_Ca_vici 151 EC36_US_AZPC_Ca_ocre 0 EC58_US_AZPC_Ph_hyat_bi 615 EC66_US_AZPC_Ca_sans 305 EC69_US_MABF_Ca_penn 534 EC91_US_AZPC_Ca_sans 82 ## 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 1385 1385 5 258 1643 6 107 1750 7 74 1824 8 25 1849 9 14 1863 10 11 1874 11 6 1880 12 4 1884 13 2 1886 14 2 1888 15 2 1890 16 0 1890 17 1 1891 18 0 1891 19 0 1891 20 1 1892 21 0 1892 22 0 1892 23 0 1892 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 0 155 0 687 0 1 188 188 276 276 2 149 486 134 544 3 98 780 106 862 4 65 1040 89 1218 5 57 1325 85 1643 6 50 1625 62 2015 7 57 2024 58 2421 8 44 2376 46 2789 9 38 2718 49 3230 10 54 3258 33 3560 11 47 3775 32 3912 12 56 4447 35 4332 13 64 5279 33 4761 14 52 6007 18 5013 15 49 6742 21 5328 16 62 7734 28 5776 17 44 8482 20 6116 18 39 9184 13 6350 19 46 10058 9 6521 20 39 10838 8 6681 21 26 11384 9 6870 22 39 12242 8 7046 23 42 13208 13 7345 24 36 14072 3 7417 25 36 14972 3 7492 26 32 15804 3 7570 27 25 16479 0 7570 28 40 17599 3 7654 29 25 18324 1 7683 30 23 19014 2 7743 31 12 19386 4 7867 32 18 19962 0 7867 33 9 20259 1 7900 34 10 20599 0 7900 35 10 20949 0 7900 36 5 21129 0 7900 37 8 21425 0 7900 38 4 21577 0 7900 39 8 21889 0 7900 40 6 22129 0 7900 41 3 22252 0 7900 42 4 22420 0 7900 43 2 22506 0 7900 44 2 22594 0 7900 45 2 22684 0 7900 46 0 22684 0 7900 47 1 22731 0 7900 48 0 22731 0 7900 49 4 22927 0 7900 50 2 23027 0 7900 51 0 23027 0 7900 52 0 23027 0 7900 53 1 23080 0 7900 54 1 23134 0 7900 55 1 23189 0 7900 56 1 23245 0 7900 57 1 23302 0 7900 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly EC01_US_AZVV_Fo_perp 7 81393 80651 16284 3163 0.005384 0.001405 2935 394 EC04_US_AZVV_Po_mar_occ 7 53733 53199 12884 2071 0.006186 0.001747 1910 299 EC05_US_AZMG_Fo_gnav 7 98507 97458 22336 4049 0.007405 0.001852 3718 191 EC07_MX_SOSJSD_Ph_rhea 7 34597 34218 9690 1121 0.008344 0.001912 1015 76 EC107_US_AZCBP_La_sp 7 292037 288946 30054 8547 0.005438 0.001455 7956 1181 EC111_US_AZCP_Cr_C 7 322688 319110 28987 8536 0.005705 0.001421 7967 1174 EC113_US_AZCP_Cr_C 7 377246 373280 32127 10491 0.004416 0.000979 10024 390 EC114_US_AZCP_Li_apic 7 233997 231304 24679 6831 0.005641 0.001467 6377 1168 EC11_MX_SOSE_Fo_gnav 7 16243 16116 4590 184 0.014202 0.003880 139 21 EC15_MX_SOSJRZ_Ph_rhea 7 18337 18163 7386 394 0.013235 0.005402 299 55 EC16_MX_SOSE_Ph_obtu 7 18714 18542 5860 279 0.014829 0.004291 221 25 EC18_US_AZPC_Ph_obtu 7 24885 24622 7934 661 0.010872 0.002418 564 151 EC19_US_AZPC_Tr_ariz 7 45529 45090 12523 1437 0.010861 0.002489 1237 292 EC20_MX_SOSJRSF_Ph_rhea 7 125545 124384 20679 4645 0.005504 0.001456 4387 266 EC21_MX_SOSJRZ_La_sp 7 65413 64675 18362 2190 0.010535 0.002446 1911 151 EC24_US_AZCH_Cr_C 7 53130 52654 11427 1599 0.008207 0.002318 1416 829 EC33_US_AZPAY_Li_apic 7 51958 51452 14846 1880 0.007753 0.001897 1697 311 EC35_US_AZPAY_Ca_vici 7 29056 28763 9698 626 0.010501 0.002801 534 151 EC36_US_AZPC_Ca_ocre 7 431 417 280 2 0.066526 0.010077 1 0 EC58_US_AZPC_Ph_hyat_bi 7 332489 329358 29366 9266 0.007055 0.001145 8691 615 EC66_US_AZPC_Ca_sans 7 271124 268375 34972 9597 0.006721 0.001544 8953 305 EC69_US_MABF_Ca_penn 7 548688 542392 40090 13582 0.007014 0.001468 12582 534 EC91_US_AZPC_Ca_sans 7 31248 30908 10931 875 0.010910 0.003416 736 82 ## Alignment matrix statistics: snps matrix size: (23, 23302), 77.84% missing sites. sequence matrix size: (23, 538972), 80.30% missing sites.