## 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 171483 filtered_by_rm_duplicates 2851 2851 168632 filtered_by_max_indels 37027 37027 131605 filtered_by_max_SNPs 2319 385 131220 filtered_by_max_shared_het 886 552 130668 filtered_by_min_sample 103055 103055 27613 total_filtered_loci 146138 143870 27613 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage 2128_Astrahmi 6336 2138_Astrahmi 5183 2205_Astrahmi 10317 2208_Aarmouri 7974 2246_Awhitemani 7003 2249_Awhitemani 7791 2729_Acristatellus 3629 2740_Acristatellus 2996 735_Adistichus 3536 980_Adistichus 3615 MMM00098_Amarcanoi 6618 MMM00099_Asmarcanoi 6169 MMM00102_Acybotes 14127 MMM00153_Acybotes 11680 MMM00186_Acybotes 13706 MMM00198_Acybotes 11089 MMM00219_Acybotes 14710 MMM00257_Acybotes 13519 MMM00277_Acybotes 11184 MMM00280_Acybotes 15452 MMM00282_Ashrevei 12120 MMM00289_Ashrevei 10402 MMM00300_Ashrevei 12451 R-190729_Aarmouri 13412 ## 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 8341 8341 5 3693 12034 6 2759 14793 7 1969 16762 8 1558 18320 9 1143 19463 10 978 20441 11 837 21278 12 784 22062 13 786 22848 14 930 23778 15 615 24393 16 807 25200 17 509 25709 18 631 26340 19 298 26638 20 535 27173 21 92 27265 22 140 27405 23 45 27450 24 163 27613 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 0 357 0 2931 0 1 499 499 2413 2413 2 642 1783 1926 6265 3 699 3880 1680 11305 4 754 6896 1481 17229 5 755 10671 1320 23829 6 788 15399 1196 31005 7 804 21027 1074 38523 8 819 27579 1014 46635 9 844 35175 905 54780 10 818 43355 894 63720 11 851 52716 791 72421 12 883 63312 802 82045 13 910 75142 790 92315 14 834 86818 700 102115 15 781 98533 718 112885 16 795 111253 602 122517 17 771 124360 684 134145 18 749 137842 597 144891 19 701 151161 627 156804 20 726 165681 486 166524 21 723 180864 457 176121 22 679 195802 445 185911 23 716 212270 376 194559 24 635 227510 319 202215 25 612 242810 314 210065 26 588 258098 261 216851 27 592 274082 246 223493 28 565 289902 212 229429 29 529 305243 207 235432 30 522 320903 188 241072 31 516 336899 162 246094 32 417 350243 128 250190 33 400 363443 109 253787 34 363 375785 91 256881 35 364 388525 80 259681 36 355 401305 58 261769 37 307 412664 68 264285 38 273 423038 53 266299 39 283 434075 34 267625 40 276 445115 33 268945 41 221 454176 38 270503 42 233 463962 29 271721 43 188 472046 16 272409 44 154 478822 19 273245 45 156 485842 9 273650 46 143 492420 13 274248 47 123 498201 9 274671 48 110 503481 3 274815 49 109 508822 1 274864 50 109 514272 1 274914 51 84 518556 0 274914 52 107 524120 1 274966 53 75 528095 1 275019 54 63 531497 1 275073 55 67 535182 0 275073 56 73 539270 0 275073 57 55 542405 0 275073 58 40 544725 0 275073 59 8 545197 0 275073 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly 2128_Astrahmi 7 2646400 2620802 102745 40704 0.005770 0.001218 39092 6336 2138_Astrahmi 7 1197289 1184291 74706 32208 0.004702 0.001259 31113 5183 2205_Astrahmi 7 3290413 3258278 116257 45792 0.006846 0.001133 43729 10317 2208_Aarmouri 7 1640542 1623451 84280 35062 0.007242 0.001393 33451 7974 2246_Awhitemani 7 1972478 1952965 96163 38491 0.006202 0.001377 37044 7003 2249_Awhitemani 7 2839590 2810299 108383 42863 0.005929 0.001269 41260 7791 2729_Acristatellus 7 6370196 6313010 150399 56413 0.008809 0.001139 53451 3629 2740_Acristatellus 7 1921340 1902701 105603 39265 0.008215 0.001209 37377 2996 735_Adistichus 7 4466609 4425184 144043 56578 0.009771 0.001238 53224 3536 980_Adistichus 7 5518624 5462767 168051 62158 0.008961 0.001216 58335 3615 MMM00098_Amarcanoi 7 3869585 3829386 128393 49427 0.004704 0.001277 46977 6618 MMM00099_Asmarcanoi 7 3151265 3117363 130714 50762 0.005406 0.001196 46921 6169 MMM00102_Acybotes 7 5453599 5396618 143783 55317 0.009635 0.001262 52667 14127 MMM00153_Acybotes 7 4302484 4259074 129829 49271 0.006704 0.001259 47155 11680 MMM00186_Acybotes 7 5289961 5239792 161030 57692 0.008787 0.001092 55012 13706 MMM00198_Acybotes 7 2487645 2460917 108985 43854 0.008929 0.001273 41907 11089 MMM00219_Acybotes 7 7208336 7136078 179738 63248 0.007994 0.001135 60369 14710 MMM00257_Acybotes 7 4401397 4356075 138274 51460 0.009678 0.001187 48993 13519 MMM00277_Acybotes 7 2604491 2575540 107302 42924 0.009248 0.001289 40929 11184 MMM00280_Acybotes 7 6633888 6559997 154939 58195 0.009753 0.001229 55293 15452 MMM00282_Ashrevei 7 3654950 3612474 123285 45935 0.005924 0.001319 44063 12120 MMM00289_Ashrevei 7 2380366 2353164 97863 38840 0.005965 0.001399 37306 10402 MMM00300_Ashrevei 7 4125862 4085319 121052 47043 0.005879 0.001237 45206 12451 R-190729_Aarmouri 7 7177983 7104166 151853 58748 0.009486 0.001199 55564 13412 ## Alignment matrix statistics: snps matrix size: (24, 545197), 60.44% missing sites. sequence matrix size: (24, 7774107), 66.05% missing sites.