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Table 1 Parameters of genetic diversity in the 115 examined cattle breeds with 46,678 SNPs

From: Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

Breed Nd nA \( \overline{nA} \) mA \( \overline{mA} \) HO HE Hdef npA \( \overline{npA} \) nspA \( \overline{nspA} \) fpA F \( \overline{F} \) AR \( \overline{AR} \) Ho(SNPs) HE(SNPs) Νe5 \( \overline{{Ne_{5} }} \) Ne50 Ne2000
Outgroups
 YAK 26 9193   1.60   0.232 0.099 − 1.350 79   70   0.406 1.056   1.29   0.030 0.029 54   123  
 GIR 24 24,111   4.19   0.486 0.464 − 0.049 78   139   0.041 0.647   2.63   0.169 0.169 48   304 3966
 NDA 27 32,136   5.58   0.569 0.574 0.009 188   185   0.032 0.334   3.15   0.228 0.230 67   524 2737
Minor Asia
 ATER 17 41,775   7.26   0.733 0.725 − 0.011 147   158   0.031 0.106   4.17   0.321 0.317 40   349 4338
 ATBC 37 51,955   9.03   0.730 0.746 0.022 294   362   0.015 0.112   4.25   0.322 0.330 96   831 5040
 ATSR 17 40,859   7.10   0.713 0.719 0.008 152   185   0.034 0.142   4.12   0.310 0.313 40   337 4274
 ATSY 7 29,941   5.20   0.696 0.683 − 0.019 43   64   0.076 0.161   4.08   0.302 0.298  
 TRG 8 31,406 44,046 5.46 7.65 0.740 0.695 − 0.064 28 191.7 65 234.8 0.069 0.071 0.117 4.10 4.18 0.327 0.308 15 64 125 2952
Greece and Cyprus
 CYP 12 27,328   4.75   0.629 0.627 − 0.004 32   55   0.115 0.261   3.41   0.271 0.271 18   119 2753
 AGT 6 17,302   3.01   0.593 0.504 − 0.178 17   23   0.206 0.329   2.74   0.244 0.218  
 CRT 11 12,688   2.20   0.518 0.373 − 0.387 11   8   0.376 0.457   2.02   0.193 0.166 8   53 1753
 NSY 7 19,634   3.41   0.608 0.551 − 0.102 11   16   0.188 0.242   2.97   0.268 0.249  
 GRB 41 49,079   8.53   0.701 0.742 0.056 142   208   0.021 0.108   4.18   0.314 0.334 85   618 4170
 KAS 4 17,185   2.99   0.656 0.520 − 0.261 23   19   0.141 0.261   2.99   0.270 0.224  
 KEA 27 33,145   5.76   0.646 0.622 − 0.038 16   23   0.026 0.150   3.31   0.295 0.284 28   160 2791
 PRG 9 26,666   4.63   0.704 0.643 − 0.094 13   31   0.073 0.096   3.58   0.319 0.293 15   109 2950
 ROG 9 25,912   4.50   0.723 0.602 − 0.202 20   29   0.100 0.094   3.36   0.321 0.270 15   114 3099
 SYK 17 37,037   6.43   0.664 0.698 0.049 67   71   0.050 0.149   3.91   0.300 0.316 29   210 3429
 KTR 19 37,105 37,879 6.45 5.89 0.651 0.685 0.050 54 58.6 74 82.6 0.045 0.175 0.178 3.80 3.54 0.292 0.308 26 40 192 3441
South-east Europe
 RHS 17 41,278   7.17   0.741 0.734 − 0.009 70   104   0.034 0.058   4.22   0.334 0.332 38   308 3905
 MKB 22 45,364   7.88   0.721 0.744 0.031 106   156   0.025 0.076   4.27   0.326 0.337 51   425 3932
 SRB 20 44,355   7.71   0.726 0.742 0.021 101   120   0.028 0.063   4.27   0.329 0.337 46   396 4099
 PRE 29 44,126   7.67   0.752 0.733 − 0.025 73   92   0.025 0.028   4.12   0.343 0.335 58   420 3933
 RMB 17 42,940   7.46   0.757 0.738 − 0.025 105   127   0.032 0.027   4.28   0.343 0.335 40   345 3825
 SHB 17 39,748   6.91   0.727 0.724 − 0.004 84   104   0.039 0.062   4.13   0.331 0.329 34   275 3664
 DGB 21 36,322   6.31   0.729 0.700 − 0.041 30   41   0.052 0.053   3.86   0.335 0.322 31   228 3398
 DBB 25 37,724   6.55   0.725 0.703 − 0.031 34   41   0.038 0.060   3.87   0.334 0.324 34   257 3298
 MAB 43 51,066   8.87   0.738 0.745 0.010 148   180   0.013 0.042   4.20   0.339 0.342 97   712 3748
 LKB 27 44,381   7.71   0.743 0.729 − 0.020 85   105   0.024 0.034   4.10   0.340 0.333 54   406 3709
 SKB 14 35,556   6.18   0.717 0.707 − 0.013 33   48   0.048 0.070   4.00   0.328 0.325 25   205 3312
 MNB 19 41,711   7.25   0.731 0.730 − 0.001 65   81   0.032 0.045   4.16   0.336 0.335 41   337 3679
 BHB 18 30,993   5.38   0.687 0.642 − 0.070 21   44   0.064 0.113   3.47   0.311 0.291 23   154 3161
 HRB 28 48,122 42,800 8.36 7.44 0.745 0.745 0.001 106 82.2 147 106.5 0.020 0.027 0.051 4.26 4.10 0.340 0.341 68 51 583 3916
East Podolian
 HRI 28 40,285   7.00   0.709 0.704 − 0.007 25   58   0.039 0.074   3.88   0.323 0.322 49   322 3414
 HRP 24 29,711   5.16   0.679 0.639 − 0.063 16   31   0.092 0.129   3.38   0.306 0.289 26   149 2959
 UKP 21 31,176 34,188 5.42 5.94 0.689 0.656 − 0.051 27 22.6 38 43.4 0.053 0.109 0.103 3.50 3.61 0.313 0.298 29 36 161 2952
Tyrrhenian
 PODO 25 43,858   7.62   0.715 0.731 0.022 75   95   0.023 0.074   4.13   0.325 0.332 56   434 3756
 CINI 30 43,242   7.51   0.715 0.727 0.016 44   77   0.025 0.075   4.06   0.325 0.331 60   434 3882
 MOSI 29 37,742   6.56   0.690 0.688 − 0.002 26   46   0.021 0.112   3.75   0.312 0.311 51   300 3546
 RSIC 24 40,468   7.03   0.739 0.719 − 0.028 21   41   0.024 0.041   4.02   0.337 0.329 45   342 3632
 MOSA 28 39,565   6.87   0.719 0.707 − 0.017 22   39   0.037 0.068   3.91   0.325 0.320 53   349 3816
 SARD 30 44,722   7.77   0.710 0.726 0.022 76   90   0.021 0.059   4.08   0.326 0.333 66   533 3633
 SBRU 10 32,211   5.60   0.697 0.689 − 0.012 15   18   0.050 0.080   3.95   0.319 0.317 21   173 3226
 CORS 30 44,708   7.77   0.722 0.724 0.002 120   119   0.022 0.050   4.06   0.331 0.330 67   535 3572
 AGER 22 34,676   6.02   0.705 0.688 − 0.025 2   15   0.023 0.072   3.76   0.327 0.320 32   222 2966
 MARE 34 37,470   6.51   0.695 0.690 − 0.006 44   47   0.028 0.105   3.74   0.313 0.312 53   294 3367
 CHI 12 32,476   5.64   0.702 0.677 − 0.037 21   42   0.042 0.093   3.81   0.320 0.310 24   166 2928
 MPIS 15 21,614   3.76   0.639 0.539 − 0.185 7   8   0.152 0.173   2.82   0.286 0.246 15   86 2203
 CALV 24 28,886   5.02   0.640 0.617 − 0.036 4   19   0.057 0.172   3.24   0.288 0.280 29   146 2841
 MCH 21 37,548   6.52   0.711 0.696 − 0.021 39   50   0.040 0.077   3.86   0.320 0.314 45   282 3311
 RMG 18 34,890   6.06   0.677 0.667 − 0.014 158   153   0.032 0.127   3.69   0.307 0.300 34   191 3245
 GARF 23 26,502   4.60   0.645 0.618 − 0.044 13   16   0.077 0.156   3.21   0.294 0.283 22   121 2833
 PONT 13 25,804   4.48   0.631 0.599 − 0.055 3   18   0.103 0.170   3.20   0.287 0.274 17   104 2466
 MODE 23 35,203   6.12   0.705 0.687 − 0.026 27   31   0.045 0.069   3.75   0.324 0.315 35   239 3111
 CABA 22 36,019   6.26   0.715 0.693 − 0.031 21   22   0.027 0.052   3.81   0.329 0.319 38   258 3132
 REGG 26 38,053   6.61   0.724 0.699 − 0.036 52   56   0.046 0.049   3.83   0.333 0.322 45   293 3503
 PMT 16 39,962   6.94   0.737 0.719 − 0.026 171   171   0.033 0.029   4.12   0.339 0.327 36   294 3284
 BURL 24 36,125 37,025 6.28 6.43 0.713 0.696 − 0.023 11 45.1 19 55.7 0.047 0.077 0.087 3.81 3.79 0.335 0.327 40 44 267 3014
Alpine
 PRDO 23 33,445   5.81   0.685 0.673 − 0.017 15   17   0.038 0.088   3.64   0.314 0.309 38   250 2912
 OVAR 31 39,534   6.87   0.731 0.706 − 0.035 30   29   0.035 0.038   3.87   0.335 0.325 48   330 3409
 REND 24 33,939   5.90   0.687 0.671 − 0.024 11   23   0.053 0.092   3.63   0.314 0.308 44   233 3181
 BPUS 24 38,621   6.71   0.717 0.703 − 0.021 25   31   0.032 0.052   3.88   0.330 0.324 42   321 3335
 PUST 24 31,615   5.49   0.701 0.667 − 0.052 16   17   0.059 0.075   3.57   0.321 0.306 32   197 3075
 SIC 26 39,920   6.94   0.732 0.714 − 0.025 28   39   0.032 0.035   3.97   0.336 0.328 49   355 3562
 PIN 29 38,594   6.71   0.714 0.701 − 0.020 27   39   0.024 0.066   3.84   0.332 0.326 50   309 3408
 TGV 50 38,939   6.76   0.700 0.690 − 0.014 36   45   0.023 0.071   3.72   0.322 0.318 67   344 3187
 MWF 46 35,855   6.23   0.710 0.675 − 0.053 21   25   0.039 0.058   3.58   0.327 0.311 45   252 3128
 OBV 35 36,925   6.42   0.695 0.682 − 0.020 17   26   0.028 0.074   3.68   0.319 0.313 66   333 3390
 BBV 50 35,287   6.13   0.656 0.643 − 0.020 10   15   0.010 0.100   3.39   0.301 0.296 65   233 2797
 DFV 50 40,079   6.96   0.692 0.684 − 0.013 26   41   0.012 0.075   3.69   0.320 0.316 98   445 3123
 FGV 50 37,494   6.51   0.704 0.682 − 0.031 15   36   0.032 0.067   3.65   0.325 0.316 64   311 3148
 VOG 18 34,749   6.04   0.721 0.688 − 0.048 12   22   0.039 0.045   3.80   0.331 0.317 33   245 3128
 ABO 22 33,385   5.80   0.706 0.666 − 0.061 21   18   0.040 0.054   3.60   0.325 0.306 37   240 3005
 MON 28 31,738   5.51   0.691 0.647 − 0.068 11   15   0.065 0.083   3.43   0.318 0.298 36   209 3003
 TAR 37 37,339 36,709 6.49 6.38 0.692 0.680 − 0.018 18 20.5 47 30.0 0.022 0.079 0.070 3.66 3.67 0.318 0.314 65 56 342 3228
France
 R DBI 29 26,163   4.55   0.606 0.578 − 0.048 25   34   0.174 0.200   2,99   0.277 0.265 28   127 2615
 SAL 26 36,384   6.32   0.668 0.667 0.000 26   40   0.043 0.117   3.62   0.305 0.305 58   321 2942
 AUB 22 37,489   6.51   0.691 0.685 − 0.008 32   49   0.028 0.079   3.79   0.317 0.314 51   349 2840
 LIM 48 42,891   7.45   0.708 0.705 − 0.003 65   75   0.015 0.066   3.85   0.326 0.325 106   563 3274
 CHR 39 43,444   7.55   0.720 0.719 − 0.001 67   63   0.018 0.061   3.97   0.335 0.335 88   482 3340
 PAR 17 36,898   6.41   0.724 0.701 − 0.033 52   53   0.035 0.044   3.93   0.333 0.322 34   262 3242
 BAQ 33 40,280   7.00   0.706 0.700 − 0.009 53   73   0.021 0.065   3.83   0.325 0.322 69   426 3291
 GAS 22 37,288 38,387 6.48 6.67 0.699 0.687 − 0.018 49 48.9 65 58.9 0.028 0.071 0.087 3.80 3.73 0.320 0.314 49 67 317 3071
Iberian
 MNRQ 30 26,609   4.62   0.637 0.605 − 0.054 28   27   0.173 0.166   3.12   0.292 0.277 29   128 2868
 MALL 30 20,486   3.56   0.556 0.521 − 0.067 14   26   0.211 0.276   2.65   0.247 0.236 19   81 2456
 NGAN 14 35,429   6.16   0.660 0.702 0.059 56   67   0.053 0.143   3.96   0.301 0.320 28   221 3208
 CANA 30 31,527   5.48   0.645 0.614 − 0.051 16   36   0.151 0.158   3.24   0.292 0.279 31   168 2801
 MARI 22 30,016   5.21   0.656 0.622 − 0.055 22   42   0.116 0.147   3.30   0.299 0.284 27   148 2686
 ALEN 10 29,018   5.04   0.654 0.655 0.001 98   86   0.080 0.166   3.67   0.297 0.294 19   136 3104
 BAR 14 32,044   5.57   0.659 0.663 0.006 29   54   0.051 0.145   3.68   0.301 0.302 31   199 2738
 MARO 19 35,039   6.09   0.687 0.677 − 0.014 40   65   0.037 0.108   3.73   0.313 0.309 45   265 3147
 SYG 11 30,662 29,205 5.33 5.07 0.670 0.667 − 0.004 43 31.3 35 43.2 0.063 0.129 0.169 3.75 3.32 0.305 0.303 20 28 149 2802
North-west Europe
 BPN 15 33,384   5.80   0.726 0.689 − 0.054 28   46   0.055 0.047   3.83   0.336 0.319 26   200 3033
 NOR 30 34,001   5.91   0.698 0.664 − 0.052 38   61   0.055 0.091   3.55   0.322 0.307 43   234 3072
 MAN 20 34,940   6.07   0.683 0.664 − 0.029 23   22   0.032 0.123   3.64   0.320 0.312 44   244 2941
 BBB 45 39,395   6.84   0.698 0.690 − 0.010 40   46   0.028 0.103   3.72   0.328 0.325 67   329 3110
 LKF 22 31,859   5.53   0.678 0.658 − 0.030 10   25   0.057 0.129   3.54   0.316 0.307 34   187 2810
 HF 50 37,888   6.58   0.696 0.685 − 0.016 14   29   0.011 0.127   3.65   0.334 0.329 72   279 2877
 GNS 16 28,903   5.02   0.634 0.623 − 0.016 89   65   0.039 0.175   3.36   0.292 0.286 29   159 2606
 JSY 49 31,507   5.47   0.624 0.619 − 0.007 20   28   0.020 0.185   3.23   0.287 0.286 74   223 2641
 HER 41 36,659   6.37   0.653 0.676 0.034 55   64   0.028 0.229   3.57   0.320 0.332 79   227 2286
 SHR 13 25,626   4.45   0.566 0.575 0.016 4   15   0.039 0.300   3.12   0.267 0.274 27   128 2131
 KRY 14 27,681   4.81   0.678 0.644 − 0.053 57   67   0.083 0.144   3.46   0.317 0.300 22   131 2698
 DXT 16 31,660   5.50   0.625 0.667 0.062 32   26   0.065 0.202   3.64   0.292 0.312 31   185 2841
 GLW 40 34,358   5.97   0.635 0.652 0.025 24   36   0.047 0.186   3.45   0.296 0.304 82   275 2744
 AAN 48 35,756   6.21   0.659 0.668 0.014 30   42   0.026 0.188   3.53   0.317 0.322 83   249 2617
 HGL 27 28,798   5.00   0.606 0.605 − 0.001 33   47   0.045 0.231   3.18   0.281 0.282 57   181 2524
 NRC 34 36,853   6.40   0.702 0.686 − 0.023 20   39   0.033 0.101   3.70   0.333 0.325 57   268 3016
 SERC 24 35,396   6.15   0.690 0.678 − 0.018 32   35   0.069 0.113   3.68   0.325 0.320 47   239 2839
 FJL 22 35,464   6.16   0.700 0.680 − 0.030 67   74   0.083 0.093   3.72   0.319 0.310 42   242 2946
 FIAY 42 37,043   6.44   0.686 0.677 − 0.014 19   46   0.018 0.111   3.61   0.323 0.318 65   281 2942
 FINE 20 38,958   6.77   0.692 0.711 0.026 78   100   0.048 0.097   3.99   0.317 0.324 41   321 3608
 FINW 35 38,966   6.77   0.696 0.693 − 0.004 59   81   0.040 0.095   3.77   0.317 0.316 56   316 3372
 FINN 18 32,166   5.59   0.719 0.670 − 0.073 27   42   0.067 0.069   3.64   0.327 0.305 27   190 3140
 YARO 20 36,065 34,908 6.27 6.06 0.707 0.686 − 0.029 58 34.9 69 47.0 0.068 0.080 0.142 3.78 3.58 0.324 0.315 39 57 246 3265
  1. Nd, number of genotyped animals; nA and \( \overline{nA} \), total and mean number of observed alleles within subpopulation; mA, nA/5756 (number of blocks); HO, average observed heterozygosity within subpopulation; HE, average expected heterozygosity within subpopulation; npA and \( \overline{npA} \), number and mean number of private alleles; nspA and \( \overline{nspA} \), number and mean number of alleles present only in two subpopulations; fpA, average frequency of private alleles, F and \( \overline{F} \), inbreeding coefficient per breed and per group; AR and \( \overline{AR} \), number and mean value of allelic richness; Ho(SNP) and HE(SNP), observed and expected heterozygosity within subpopulation by SNPs; Ne5 and \( \overline{{Ne_{5} }} \), effective population number for five generations back per breed and per group; Ne50 and Ne2000, effective population number for fifty and two thousand generations back
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