S2 Appendix. ipyrad summary statistics. ## 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 520248 filtered_by_rm_duplicates 3488 3488 516760 filtered_by_max_indels 15852 15852 500908 filtered_by_max_SNPs 5181 4575 496333 filtered_by_max_shared_het 4121 3919 492414 filtered_by_min_sample 116901 116901 375513 total_filtered_loci 145543 144735 375513 ## The number of loci recovered for each Sample. ## ipyrad API location: [assembly].stats_dfs.s7_samples sample_coverage A 3266 D 1 ES_R 17783 ES_V 130056 Guat_B 151612 Guat_C 62324 Guat_E 167879 Guat_F 65820 Hond_M 112185 Hond_Q 152003 Hond_X 63859 Hond_Y 47461 Mex_01 71957 Mex_09 155946 Mex_100 2587 Mex_101 155980 Mex_102 9268 Mex_103 18322 Mex_104 383 Mex_105 161440 Mex_106 8651 Mex_107 16209 Mex_108 157102 Mex_109 18771 Mex_11 151346 Mex_110 165218 Mex_111 27944 Mex_112 81375 Mex_18 152405 Mex_19 99003 Mex_21 155967 Mex_23 118586 Mex_24 129570 Mex_25 114989 Mex_26 61375 Mex_27 34847 Mex_28 23003 Mex_29 154191 Mex_30 136321 Mex_31 63949 Mex_32 36771 Mex_33 22262 Mex_34 6509 Mex_35 94579 Mex_36 0 Mex_37 143905 Mex_38 3238 Mex_39 99990 Mex_40 12959 Mex_41 74156 Mex_42 61857 Mex_43 138117 Mex_44 75410 Mex_45 169 Mex_46 38093 Mex_47 56294 Mex_48 98351 Mex_49 38058 Mex_50 119647 Mex_51 151207 Mex_52 50710 Mex_53 82175 Mex_54 1698 Mex_55 129052 Mex_56 144289 Mex_57 107377 Mex_58 145801 Mex_59 145005 Mex_60 64240 Mex_61 71091 Mex_62 152783 Mex_63 153316 Mex_64 117023 Mex_65 64027 Mex_66 30425 Mex_67 9660 Mex_68 115398 Mex_69 98297 Mex_70 108546 Mex_71 15059 Mex_72 2063 Mex_73 144327 Mex_74 23823 Mex_75 13579 Mex_76 7133 Mex_77 50741 Mex_78 6223 Mex_79 14144 Mex_80 20178 Mex_81 64686 Mex_82 109444 Mex_83 125345 Mex_84 106961 Mex_85 21202 Mex_86 149973 Mex_87 138684 Mex_88 6968 Mex_89 35550 Mex_90 1213 Mex_91 4378 Mex_92 135988 Mex_93 65993 Mex_94 148385 Mex_95 96179 Mex_96 142012 Mex_97 148105 Mex_98 141034 Mex_99 148373 Mex_F1 87355 Mex_F2 77351 Mex_F3 27379 Mex_F4 63231 Mex_F5 152078 Mex_G01 101911 Mex_G02 50620 Mex_G03 40726 Mex_G06 51029 Mex_G07 8916 Mex_G08 39282 Mex_G10 6735 Mex_G11 98684 Mex_G12 865 Mex_G13 106336 Mex_G14 146742 Mex_G15 118026 Mex_G16 12994 Mex_G17 117067 Mex_G18 9152 Mex_G19 149844 Mex_G20 125353 Mex_G21 2 Mex_G22 71139 Mex_G23 72513 Mex_G24 8076 Mex_G25 1032 Mex_G26 54353 Mex_G28 193 Mex_G30 3 Mex_G31 58 Mex_G34 6010 Mex_G35 72532 Mex_G36 121271 Mex_G37 132502 Mex_G38 66191 Mex_G39 128 Mex_G40 36552 Mex_G41 31197 Mex_G42 161883 Mex_G43 77882 Mex_G44 5883 Mex_G45 88644 Mex_G47 126244 Mex_G48 49739 Mex_G49 64409 Mex_G5 127760 Mex_G50 24814 Mex_G51 66231 Mex_G52 150949 Mex_G53 153348 Mex_G54 142415 Mex_G55 69769 Mex_G56 7007 Mex_G57 160593 Mex_G58 94962 Mex_G59 74719 Mex_G60 97235 Mex_G61 64592 Mex_G62 31236 Mex_G63 150359 Mex_G64 126490 Mex_G65 58775 Mex_G66 12996 Mex_G67 258 Mex_G68 104791 Mex_G69 129592 Mex_G70 115793 Mex_G71 98150 Mex_G72 156903 Mex_G73 6109 Mex_G74 148412 Mex_G75 8822 Mex_G76 44867 Mex_G9 100454 Mex_T10 152210 Mex_T15 67858 Mex_T20 95634 Mex_T25 145536 Mex_T5 3560 Poecilia_mexicana_W 23972 S 4199 T 278 U 1404 brhab 55670 pinfans_1 9445 pinfans_2 25572 pinfans_3 17450 pinfans_4 30023 ## 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 29184 29184 5 20195 49379 6 16789 66168 7 13966 80134 8 11949 92083 9 7901 99984 10 5995 105979 11 5193 111172 12 4945 116117 13 4528 120645 14 4329 124974 15 4215 129189 16 4028 133217 17 3891 137108 18 3833 140941 19 3860 144801 20 3722 148523 21 3731 152254 22 3592 155846 23 3593 159439 24 3442 162881 25 3428 166309 26 3408 169717 27 3446 173163 28 3365 176528 29 3283 179811 30 3359 183170 31 3314 186484 32 3327 189811 33 3369 193180 34 3134 196314 35 3347 199661 36 3319 202980 37 3419 206399 38 3391 209790 39 3372 213162 40 3457 216619 41 3358 219977 42 3472 223449 43 3421 226870 44 3259 230129 45 3423 233552 46 3331 236883 47 3426 240309 48 3304 243613 49 3334 246947 50 3174 250121 51 3193 253314 52 3208 256522 53 3275 259797 54 3198 262995 55 3188 266183 56 3010 269193 57 3055 272248 58 2895 275143 59 2972 278115 60 2863 280978 61 2798 283776 62 2799 286575 63 2654 289229 64 2547 291776 65 2548 294324 66 2508 296832 67 2545 299377 68 2407 301784 69 2392 304176 70 2447 306623 71 2196 308819 72 2296 311115 73 2193 313308 74 2252 315560 75 2142 317702 76 2067 319769 77 2092 321861 78 2040 323901 79 1933 325834 80 1886 327720 81 1916 329636 82 1825 331461 83 1835 333296 84 1710 335006 85 1753 336759 86 1587 338346 87 1621 339967 88 1595 341562 89 1427 342989 90 1447 344436 91 1394 345830 92 1427 347257 93 1404 348661 94 1325 349986 95 1329 351315 96 1221 352536 97 1188 353724 98 1130 354854 99 1128 355982 100 1105 357087 101 1031 358118 102 1016 359134 103 1021 360155 104 886 361041 105 879 361920 106 843 362763 107 822 363585 108 794 364379 109 772 365151 110 714 365865 111 688 366553 112 687 367240 113 653 367893 114 610 368503 115 599 369102 116 544 369646 117 510 370156 118 447 370603 119 492 371095 120 406 371501 121 413 371914 122 356 372270 123 334 372604 124 307 372911 125 301 373212 126 249 373461 127 216 373677 128 216 373893 129 201 374094 130 174 374268 131 150 374418 132 156 374574 133 131 374705 134 104 374809 135 98 374907 136 79 374986 137 87 375073 138 52 375125 139 73 375198 140 44 375242 141 42 375284 142 42 375326 143 22 375348 144 40 375388 145 28 375416 146 23 375439 147 12 375451 148 15 375466 149 8 375474 150 13 375487 151 6 375493 152 5 375498 153 5 375503 154 2 375505 155 3 375508 156 1 375509 157 1 375510 158 0 375510 159 2 375512 160 0 375512 161 0 375512 162 1 375513 163 0 375513 164 0 375513 165 0 375513 166 0 375513 167 0 375513 168 0 375513 169 0 375513 170 0 375513 171 0 375513 172 0 375513 173 0 375513 174 0 375513 175 0 375513 176 0 375513 177 0 375513 178 0 375513 179 0 375513 180 0 375513 181 0 375513 182 0 375513 183 0 375513 184 0 375513 185 0 375513 186 0 375513 187 0 375513 188 0 375513 189 0 375513 190 0 375513 191 0 375513 192 0 375513 193 0 375513 194 0 375513 195 0 375513 196 0 375513 197 0 375513 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 66375 0 119168 0 1 51119 51119 67698 67698 2 42592 136303 48253 164204 3 36457 245674 35906 271922 4 31609 372110 27784 383058 5 27524 509730 21122 488668 6 23144 648594 15905 584098 7 19684 786382 11962 667832 8 16738 920286 8673 737216 9 13839 1044837 6278 793718 10 11186 1156697 4540 839118 11 9084 1256621 3190 874208 12 7315 1344401 2118 899624 13 5894 1421023 1442 918370 14 4548 1484695 781 929304 15 3331 1534660 431 935769 16 2530 1575140 184 938713 17 1904 1607508 62 939767 18 509 1616670 6 939875 19 65 1617905 5 939970 20 29 1618485 4 940050 21 12 1618737 0 940050 22 17 1619111 1 940072 23 5 1619226 0 940072 24 1 1619250 0 940072 25 2 1619300 0 940072 ## Final Sample stats summary state reads_raw reads_passed_filter clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly A 7 331751 327738 181788 4333 0.018096 0.002563 3786 3266 D 7 2763 2661 2497 3 0.034301 0.013493 1 1 ES_R 7 525861 524036 191937 21037 0.011839 0.002242 20077 17783 ES_V 7 2961415 2787468 335249 151910 0.024062 0.001991 147627 130056 Guat_B 7 5231031 5131357 551915 185126 0.054117 0.002713 169254 151612 Guat_C 7 1480752 1445450 366665 72659 0.019760 0.002560 69225 62324 Guat_E 7 6484803 6185285 546033 203622 0.037178 0.001964 191173 167879 Guat_F 7 1602491 1569521 389916 76894 0.017716 0.002345 72993 65820 Hond_M 7 3683636 3587905 413737 137516 0.018912 0.002118 130761 112185 Hond_Q 7 6525630 6281885 546097 188723 0.052405 0.002710 174306 152003 Hond_X 7 1720725 1704322 359270 75827 0.024198 0.002092 70638 63859 Hond_Y 7 1204052 1196194 302320 55878 0.014796 0.002283 53286 47461 Mex_01 7 1643133 1575684 323196 85537 0.014151 0.002126 81137 71957 Mex_09 7 17244664 16197678 726760 200131 0.062036 0.002238 179031 155946 Mex_100 7 182435 179756 93997 3156 0.009447 0.001879 2938 2587 Mex_101 7 11142404 10618394 525526 184670 0.039766 0.001377 174346 155980 Mex_102 7 371483 363040 148557 10848 0.009256 0.001600 10312 9268 Mex_103 7 589326 583389 226607 21524 0.013271 0.002348 20381 18322 Mex_104 7 140848 138690 92339 572 0.023707 0.004585 456 383 Mex_105 7 13264789 13058493 549591 201232 0.046568 0.002117 181593 161440 Mex_106 7 420543 412874 187232 10346 0.010594 0.001913 9636 8651 Mex_107 7 536287 533462 203977 19089 0.012891 0.002250 18140 16209 Mex_108 7 7875445 7753074 544907 190474 0.048089 0.002089 173232 157102 Mex_109 7 634271 629304 236763 22414 0.013391 0.002390 20931 18771 Mex_11 7 7224284 6903976 419935 179409 0.033788 0.001526 171193 151346 Mex_110 7 10818099 10636724 532827 200672 0.048476 0.001957 182602 165218 Mex_111 7 845505 835038 222062 32503 0.014433 0.001756 31068 27944 Mex_112 7 1810299 1741209 317333 93572 0.014661 0.001748 90024 81375 Mex_18 7 5263251 5120719 521790 182693 0.035943 0.001902 171223 152405 Mex_19 7 2232601 2049714 418487 117980 0.020472 0.003803 109944 99003 Mex_21 7 7126860 6777773 688227 201075 0.050712 0.003186 178749 155967 Mex_23 7 2978250 2888360 386759 140597 0.027008 0.001855 130613 118586 Mex_24 7 5365518 5306253 539069 156670 0.046582 0.002323 141952 129570 Mex_25 7 3066611 2970115 394782 132913 0.031415 0.001691 127067 114989 Mex_26 7 2054982 2038535 347952 72455 0.024244 0.001719 67672 61375 Mex_27 7 900063 873331 259493 40275 0.015043 0.002286 38235 34847 Mex_28 7 803298 799087 216573 27485 0.016779 0.002094 25658 23003 Mex_29 7 7862591 7706438 551997 192019 0.052627 0.002148 171441 154191 Mex_30 7 3065677 2878934 353045 156879 0.022798 0.001655 152212 136321 Mex_31 7 2083716 2072944 392434 75561 0.023695 0.001939 70601 63949 Mex_32 7 1007863 991768 279581 42676 0.015417 0.001998 40643 36771 Mex_33 7 687286 678320 245641 25996 0.013580 0.002442 24540 22262 Mex_34 7 312008 307956 145801 7754 0.008786 0.001891 7228 6509 Mex_35 7 3304184 3277889 415784 110946 0.034471 0.001751 103930 94579 Mex_36 7 1701 1646 1468 2 0.063227 0.008720 1 0 Mex_37 7 6065489 5887473 457067 172965 0.046144 0.001543 161063 143905 Mex_38 7 263372 257927 135196 4032 0.009751 0.002593 3658 3238 Mex_39 7 2134712 2061584 335927 113495 0.022404 0.001950 109934 99990 Mex_40 7 508705 499918 200961 15148 0.012501 0.002459 14353 12959 Mex_41 7 2886216 2868807 369935 86538 0.028277 0.001593 81420 74156 Mex_42 7 1604872 1585856 327836 70867 0.018774 0.001862 68077 61857 Mex_43 7 6536394 6497025 549820 166086 0.051771 0.002390 149565 138117 Mex_44 7 2645247 2620556 389004 87188 0.028092 0.001632 82890 75410 Mex_45 7 79832 77669 55312 267 0.021084 0.005168 211 169 Mex_46 7 1022750 1007370 268900 44137 0.012508 0.001997 42317 38093 Mex_47 7 2001812 1991652 323040 66167 0.021612 0.001750 62395 56294 Mex_48 7 4518105 4500138 488935 116889 0.035075 0.001862 107737 98351 Mex_49 7 1032867 1023250 275476 43955 0.015761 0.001931 42159 38058 Mex_50 7 4947735 4919131 504205 141671 0.043434 0.002080 129966 119647 Mex_51 7 6162717 6041551 496040 179302 0.043965 0.001841 166689 151207 Mex_52 7 1563042 1555095 294623 58873 0.017896 0.001566 56301 50710 Mex_53 7 2464900 2435225 362754 95058 0.023262 0.001689 90417 82175 Mex_54 7 132697 131677 74716 2162 0.010044 0.002394 1944 1698 Mex_55 7 7286411 7238694 596500 157723 0.047617 0.002274 141634 129052 Mex_56 7 4834801 4635759 459022 167556 0.037680 0.001665 160568 144289 Mex_57 7 5056279 5033632 461499 127070 0.035619 0.001769 116976 107377 Mex_58 7 5298742 5226884 483307 172781 0.045482 0.002048 159831 145801 Mex_59 7 6385873 6307535 489276 172740 0.048773 0.001986 158699 145005 Mex_60 7 2036943 2027328 370690 74260 0.024163 0.001592 70835 64240 Mex_61 7 1964244 1934502 337134 81962 0.018687 0.001683 78580 71091 Mex_62 7 6994584 6898723 491937 182981 0.047347 0.002055 167555 152783 Mex_63 7 9924786 9802240 677997 194531 0.055958 0.002905 169975 153316 Mex_64 7 5386458 5341674 475342 139096 0.040499 0.001949 128131 117023 Mex_65 7 1369742 1298348 295136 73368 0.016304 0.002413 70927 64027 Mex_66 7 937653 931899 254713 35610 0.013563 0.001884 34090 30425 Mex_67 7 395760 392171 168097 11443 0.007749 0.001683 10855 9660 Mex_68 7 2737146 2609037 386859 133630 0.030001 0.002309 127676 115398 Mex_69 7 2552615 2520765 371922 112830 0.029401 0.001800 107770 98297 Mex_70 7 4050712 4010686 401051 126708 0.030529 0.001704 118749 108546 Mex_71 7 513289 507827 199512 17569 0.011232 0.002348 16761 15059 Mex_72 7 224458 221937 122285 2589 0.011458 0.002526 2335 2063 Mex_73 7 5667490 5516726 502259 176699 0.049682 0.002011 159054 144327 Mex_74 7 715556 712431 229583 28623 0.013724 0.002395 26667 23823 Mex_75 7 496452 484836 188571 15788 0.011810 0.002153 14984 13579 Mex_76 7 349813 346218 156436 8555 0.008071 0.002085 8056 7133 Mex_77 7 1429830 1405853 325207 58938 0.018117 0.002112 55992 50741 Mex_78 7 300015 293663 137351 7497 0.008203 0.001862 7006 6223 Mex_79 7 500170 492641 187302 16505 0.012715 0.002359 15680 14144 Mex_80 7 592369 588310 188141 23553 0.011691 0.001970 22556 20178 Mex_81 7 2576346 2551185 360313 76721 0.019825 0.001735 72454 64686 Mex_82 7 4498000 4458253 447721 128635 0.033750 0.001772 119889 109444 Mex_83 7 4918233 4840153 426495 147043 0.032715 0.001791 137556 125345 Mex_84 7 4005220 3964071 444418 125177 0.033869 0.001749 117247 106961 Mex_85 7 687685 684793 197983 26151 0.016359 0.002073 23463 21202 Mex_86 7 6823790 6729204 544560 179959 0.045747 0.001952 164687 149973 Mex_87 7 4450287 4363466 453203 163367 0.043523 0.002080 151938 138684 Mex_88 7 392063 384638 176337 8256 0.009521 0.001964 7734 6968 Mex_89 7 1102570 1094795 297675 41459 0.013997 0.001990 39469 35550 Mex_90 7 122181 120755 73652 1485 0.009213 0.002013 1352 1213 Mex_91 7 308850 298485 147938 5355 0.009398 0.002099 4945 4378 Mex_92 7 3614524 3472563 376790 156081 0.026658 0.001534 150764 135988 Mex_93 7 1932251 1899982 338706 76538 0.018107 0.001784 73033 65993 Mex_94 7 5642831 5528700 462902 174296 0.043417 0.001574 163843 148385 Mex_95 7 2508024 2465368 348373 110439 0.022341 0.001657 105591 96179 Mex_96 7 5529831 5408024 476558 168564 0.040273 0.001927 156754 142012 Mex_97 7 6789506 6551814 503617 177214 0.045923 0.001754 164713 148105 Mex_98 7 4964049 4754744 445997 163787 0.034791 0.001432 156892 141034 Mex_99 7 6041643 5919784 503482 175335 0.041562 0.001792 163283 148373 Mex_F1 7 2826027 2804496 624788 108640 0.028865 0.002361 101845 87355 Mex_F2 7 2465745 2442755 539197 94804 0.024037 0.002294 89437 77351 Mex_F3 7 904568 877107 329242 32314 0.014641 0.003022 30662 27379 Mex_F4 7 1611516 1571505 414852 74311 0.017618 0.002469 71129 63231 Mex_F5 7 6219148 5957388 621361 206552 0.037444 0.002001 194595 152078 Mex_G01 7 3838588 3805918 478110 120834 0.032085 0.001898 112860 101911 Mex_G02 7 1493993 1472149 342785 59326 0.014260 0.002173 56162 50620 Mex_G03 7 1065229 1046708 308554 46967 0.014406 0.002146 44976 40726 Mex_G06 7 1372967 1358113 373424 59847 0.015659 0.002691 56310 51029 Mex_G07 7 420629 406592 183165 10537 0.008141 0.001881 10030 8916 Mex_G08 7 1246577 1229464 362487 46337 0.013942 0.002078 44205 39282 Mex_G10 7 544336 521895 245758 8212 0.017241 0.003200 7522 6735 Mex_G11 7 2263874 2177689 459299 113721 0.034447 0.002601 108679 98684 Mex_G12 7 248672 226465 137964 1249 0.032278 0.006179 1045 865 Mex_G13 7 2539297 2393495 459462 129086 0.041477 0.003080 117787 106336 Mex_G14 7 8171899 7670634 648325 182925 0.058412 0.002427 163969 146742 Mex_G15 7 2859525 2627984 446564 137388 0.034930 0.002292 131707 118026 Mex_G16 7 559817 546146 233784 15417 0.018664 0.002841 14493 12994 Mex_G17 7 2835667 2744470 468053 139906 0.036736 0.002409 128024 117067 Mex_G18 7 579737 554724 256291 11148 0.015815 0.002899 10242 9152 Mex_G19 7 5065961 4831300 585635 179898 0.048344 0.002343 166292 149844 Mex_G20 7 2957102 2843492 490397 146141 0.041307 0.002728 138298 125353 Mex_G21 7 22483 17066 15193 17 0.030121 0.023397 7 2 Mex_G22 7 1739857 1705473 389324 82025 0.022325 0.002370 78750 71139 Mex_G23 7 1536567 1450831 356414 84337 0.020251 0.003258 80829 72513 Mex_G24 7 544460 504130 225699 9896 0.016699 0.003249 9209 8076 Mex_G25 7 281182 253255 157596 1506 0.020773 0.005687 1238 1032 Mex_G26 7 1368385 1321117 354211 64646 0.017306 0.003092 60726 54353 Mex_G28 7 161470 144433 100196 343 0.036400 0.009376 254 193 Mex_G30 7 18746 16080 14698 18 0.043464 0.022317 8 3 Mex_G31 7 121193 115941 89103 161 0.044079 0.010940 93 58 Mex_G34 7 351135 342643 168886 7427 0.010988 0.002249 6820 6010 Mex_G35 7 1557597 1516471 358245 83718 0.020592 0.002529 80267 72532 Mex_G36 7 2795158 2747248 492389 139134 0.035714 0.002214 132122 121271 Mex_G37 7 3269369 3227234 494123 152381 0.037129 0.002443 143934 132502 Mex_G38 7 1767711 1740362 420680 76521 0.024184 0.001973 72580 66191 Mex_G39 7 136281 130641 97651 252 0.034384 0.010117 171 128 Mex_G40 7 1018494 993767 317770 42349 0.019181 0.002487 40223 36552 Mex_G41 7 926647 906115 288064 36437 0.019408 0.002088 34449 31197 Mex_G42 7 14947005 14207134 700794 205119 0.062397 0.001921 183511 161883 Mex_G43 7 1632584 1565680 379744 89774 0.028032 0.002287 85432 77882 Mex_G44 7 441753 426606 211739 7234 0.013176 0.002471 6609 5883 Mex_G45 7 1950394 1888833 403364 101480 0.028032 0.002287 97099 88644 Mex_G47 7 3003432 2907819 515510 146350 0.038476 0.002714 139208 126244 Mex_G48 7 1306271 1268721 407776 57776 0.017760 0.002973 54866 49739 Mex_G49 7 1687864 1677344 404295 73965 0.019105 0.002063 71007 64409 Mex_G5 7 3322609 3245641 438309 147709 0.031210 0.002004 140102 127760 Mex_G50 7 830424 813520 313773 28858 0.013915 0.002830 27503 24814 Mex_G51 7 1807806 1786511 459962 76220 0.018991 0.002162 73119 66231 Mex_G52 7 7793085 7618533 647669 189077 0.061912 0.002408 170857 150949 Mex_G53 7 5064700 4936308 635658 190032 0.053467 0.002663 168987 153348 Mex_G54 7 5492733 5414849 790764 170733 0.042431 0.002397 158523 142415 Mex_G55 7 1662594 1602308 379004 79385 0.023092 0.002384 76699 69769 Mex_G56 7 605238 597360 356906 8723 0.010802 0.002376 8030 7007 Mex_G57 7 5033801 4859128 562741 191297 0.048905 0.001990 177495 160593 Mex_G58 7 2627347 2589232 487599 110256 0.031047 0.002047 103869 94962 Mex_G59 7 1903570 1869226 382371 86312 0.021617 0.001934 82049 74719 Mex_G60 7 2397506 2258849 467683 112197 0.030267 0.002343 106166 97235 Mex_G61 7 1566322 1535554 426813 74630 0.024407 0.002551 70421 64592 Mex_G62 7 944280 934652 342733 36211 0.017736 0.002287 34350 31236 Mex_G63 7 4225764 4109071 537979 177035 0.046641 0.002292 165544 150359 Mex_G64 7 3148129 3072538 498821 147772 0.035233 0.002335 138437 126490 Mex_G65 7 1419179 1381753 401732 67468 0.022094 0.002557 64284 58775 Mex_G66 7 645006 619759 271018 15373 0.020806 0.003409 14310 12996 Mex_G67 7 153317 147044 103930 438 0.031565 0.007302 323 258 Mex_G68 7 2279942 2208278 430916 120292 0.027520 0.002142 115271 104791 Mex_G69 7 3308021 3221609 473026 150201 0.036082 0.002269 142699 129592 Mex_G70 7 2769785 2646778 423669 134199 0.035014 0.002009 128101 115793 Mex_G71 7 2308989 2257660 467869 113107 0.030013 0.002401 107346 98150 Mex_G72 7 5547231 5440763 609295 188534 0.047000 0.002157 173458 156903 Mex_G73 7 428120 416833 217780 7551 0.011622 0.002254 6924 6109 Mex_G74 7 5921776 5625211 581404 181466 0.053874 0.002318 165209 148412 Mex_G75 7 497577 486229 232449 10638 0.011557 0.002198 9859 8822 Mex_G76 7 1183711 1158634 331228 52049 0.020360 0.002100 49396 44867 Mex_G9 7 2284903 2088750 393590 117755 0.035330 0.002854 111776 100454 Mex_T10 7 6617645 6382367 603569 215161 0.045857 0.002152 197893 152210 Mex_T15 7 1715411 1675992 374302 80299 0.020518 0.002188 76999 67858 Mex_T20 7 2369769 2313795 453569 114371 0.024472 0.002240 109716 95634 Mex_T25 7 6574425 6408905 625720 199832 0.039329 0.001987 186716 145536 Mex_T5 7 421461 407437 215699 4571 0.013310 0.002881 4118 3560 Poecilia_mexicana_W 7 2322872 2310313 391026 77721 0.026411 0.002194 71151 23972 S 7 432348 425376 228198 5335 0.014820 0.003047 4784 4199 T 7 273501 264260 175134 1109 0.042471 0.012160 646 278 U 7 262709 258382 164740 1898 0.018947 0.003691 1626 1404 brhab 7 5392742 5376166 401382 136009 0.026706 0.001676 125530 55670 pinfans_1 7 415516 414654 139340 16225 0.012549 0.002539 15206 9445 pinfans_2 7 1319922 1317942 307021 58452 0.012828 0.001646 55908 25572 pinfans_3 7 796495 794565 237278 34901 0.012971 0.001866 33338 17450 pinfans_4 7 2410750 2404560 455557 95718 0.019725 0.002394 87664 30023 ## Alignment matrix statistics: snps matrix size: (197, 1619300), 76.49% missing sites. sequence matrix size: (197, 31462914), 80.69% missing sites.