# Last edited on 2019-05-23 08:37:35 by stolfilocal # Haak et al https://doi.org/10.1101/013433 # OnlineTable1 from https://www.biorxiv.org/highwire/filestream/3855/field_highwire_adjunct_files/1/013433-2.xlsx # Renamings to avoid non-ascii characters: # Alsónyék-Bátaszék, --> Mérnöki Alsonyek-Bataszek, Mernoki # Viesenhäuser Hof, Stuttgart-Mühlhausen --> Viesenhaeuser Hof, Stuttgart-Muehlhausen S0271 | I0172 | ESP24 | Adelaide | plus | 6 | Esperstedt_MN | Esperstedt | 3360-3086 calBCE | Germany | 51.4200000000000 | 11.6800000000000 | 1633075 | 1496014 | 12117 | 52 | 659748 | 522833 | 684 | 0.010 | T2b | 0.978 | [ 0.9712392,0.9832812 ] | 77 | 69045754 | 67483405 | 47942665 | 15614765 | 0.034 | 1760 | 1881 | 0.98 | 39.65 | 67 | passed | 94 | .. S0662 | I0172 | ESP24 | Adelaide | half | 10 | Esperstedt_MN | Esperstedt | 3360-3086 calBCE | Germany | 51.4200000000000 | 11.6800000000000 | n/a | n/a | n/a | n/a | 1931421 | 1122110 | 1160 | 0.157 | T2b | 0.985 | [ 0.9784576,0.9888104 ] | 84 | 50368706 | 48129029 | 21194310 | 7470866 | 0.146 | 1771 | 1917 | 0.99 | 18.97 | 50 | passed | n/a | .. S0663 | I0172 | ESP24 | Adelaide | half | 10 | Esperstedt_MN | Esperstedt | 3360-3086 calBCE | Germany | 51.4200000000000 | 11.6800000000000 | n/a | n/a | n/a | n/a | 1586649 | 892738 | 686 | 0.120 | T2b | 0.959 | [ 0.9487352,0.9659838 ] | 84 | 32552671 | 31319256 | 15135320 | 4418916 | 0.114 | 1733 | 1823 | 0.98 | 11.22 | 55 | passed | n/a | .. S0560 | I0560 | QLB18A | Adelaide | half | 9 | Baalberge_MN | Quedlinburg_IX | 3640-3510 calBCE | Germany | 51.7900000000000 | 11.1400000000000 | 869858 | 549364 | 3884 | 71 | 869858 | 475028 | 227 | 0.116 | T2e1 | 0.999 | [ 0.9972151,0.9999338 ] | 79 | 5096094 | 4211166 | 3023603 | 203704 | 0.089 | 692 | 1 | 0.38 | 0.52 | 71 | passed | 133 | .. S0559 | I0559 | QLB15D | Adelaide | half | 9 | Baalberge_MN | Quedlinburg_IX | 3645-3537 calBCE | Germany | 51.7900000000000 | 11.1400000000000 | 368041 | 212960 | 400 | 74 | 368041 | 207451 | 160 | 0.171 | HV6'17 | 1.000 | [ 0.9969851,0.9999764 ] | 76 | 2405922 | 1526890 | 1273074 | 85415 | 0.165 | 215 | 168 | 0.19 | 0.22 | 73 | passed | 487 | .. S0807 | I0807 | ESP30 | Adelaide | half | 11 | Baalberge_MN | Esperstedt | 3887-3797 calBCE | Germany | 51.4200000000000 | 11.6800000000000 | 1042276 | 121778 | 918 | 48 | 872288 | 525358 | 48.9 | 0.097 | H1e1a | 0.986 | [ 0.9793746,0.9905356 ] | 52 | 1576641 | 564693 | 266668 | 42502 | 0.098 | 105 | 84 | 0.10 | 0.11 | 48 | passed | 192 | .. S0486 | I0405 | Mina3 | Adelaide | plus | 8 | Spain_MN | La_Mina | 3900-3600 BCE | Spain | 41.2522000000000 | -2.3262200000000 | 48777 | 325 | 3 | 57 | 328899 | 211762 | 412 | 0.028 | K1a1b1 | 0.997 | [ 0.9938944,0.9981828 ] | 78 | 3562784 | 2460378 | 1963897 | 235655 | 0.056 | 353 | 359 | 0.38 | 0.60 | 58 | passed | 8962 | .. S0487 | I0406 | Mina4 | Adelaide | plus | 8 | Spain_MN | La_Mina | 3900-3600 BCE | Spain | 41.2522000000000 | -2.3262200000000 | 53167 | 4455 | 41 | 57 | 394486 | 247185 | 518 | 0.028 | H1 | 0.993 | [ 0.9878292,0.9957051 ] | 76 | 28046100 | 24763536 | 19113881 | 3874362 | 0.055 | 1470 | 1472 | 0.91 | 9.84 | 62 | passed | 884 | .. S0488 | I0407 | Mina6 | Adelaide | plus | 8 | Spain_MN | La_Mina | 3900-3600 BCE | Spain | 41.2522000000000 | -2.3262200000000 | 1938 | 118 | 2 | 56 | 178929 | 118868 | 357 | 0.026 | K1b1a1 | 0.998 | [ 0.9957543,0.9990230 ] | 89 | 5838734 | 4959613 | 3889708 | 981737 | 0.055 | 1054 | 1 | 0.66 | 2.49 | 64 | passed | 646 | .. S0489 | I0408 | Mina18 | Adelaide | plus | 8 | Spain_MN | La_Mina | 3900-3600 BCE | Spain | 41.2522000000000 | -2.3262200000000 | 7046 | 2033 | 15 | 55 | 311789 | 193512 | 507 | 0.025 | pre-U5b1i | 0.951 | [ 0.9419401,0.9593910 ] | 77 | 42535191 | 39072604 | 28735154 | 10452103 | 0.047 | 1625 | 2 | 0.92 | 26.54 | 62 | passed | 317 | Manual examination indicates that the apparent signal of mt-DNA contamination is driven by reads aligning to nuclear mitochondrial insertions S0666 | I0408 | Mina18 | Adelaide | half | 10 | Spain_MN | La_Mina | 3900-3600 BCE | Spain | 41.2522000000000 | -2.3262200000000 | n/a | n/a | n/a | n/a | 1206977 | 500168 | 327 | 0.127 | pre-U5b1i | 0.940 | [ 0.9300015,0.9481330 ] | 75 | 11116022 | 8228231 | 3877034 | 1126614 | 0.136 | 1237 | 2 | 0.74 | 2.86 | 52 | passed | n/a | Manual examination indicates that the apparent signal of mt-DNA contamination is driven by reads aligning to nuclear mitochondrial insertions S0667 | I0408 | Mina18 | Adelaide | half | 10 | Spain_MN | La_Mina | 3900-3600 BCE | Spain | 41.2522000000000 | -2.3262200000000 | n/a | n/a | n/a | n/a | 1513113 | 614970 | 407 | 0.135 | pre-U5b1i | 0.953 | [ 0.9441260,0.9603407 ] | 77 | 19508455 | 13735932 | 6313401 | 1629130 | 0.134 | 1383 | 1 | 0.82 | 4.14 | 52 | passed | n/a | Manual examination indicates that the apparent signal of mt-DNA contamination is driven by reads aligning to nuclear mitochondrial insertions S0273 | I0100 | HAL4 | Adelaide | plus | 6 | LBK_EN | Halberstadt-Sonntagsfeld | 5032-4946 calBCE | Germany | 51.8900000000000 | 11.0400000000000 | 1731420 | 1509839 | 14069 | 59 | 871967 | 722779 | 1360 | 0.009 | N1a1a1a | 0.995 | [ 0.9912666,0.9972262 ] | 93 | 30508586 | 29713001 | 20810651 | 5265127 | 0.036 | 1748 | 1 | 0.96 | 13.37 | 62 | passed | 84 | .. S0821 | I0821 | HAL24 | Adelaide | half | 11 | LBK_EN | Halberstadt-Sonntagsfeld | 5034-4942 calBCE | Germany | 51.8958333333333 | 11.0466666666667 | 602355 | 80567 | 654 | 61 | 346347 | 236123 | 136 | 0.100 | pre-X2d1 | 0.995 | [ 0.9910107,0.9972221 ] | 62 | 11983456 | 6003323 | 3406373 | 79015 | 0.069 | 155 | 175 | 0.17 | 0.20 | 58 | passed | 262 | .. S0659 | I0659 | HAL2 | Adelaide | half | 10 | LBK_EN | Halberstadt-Sonntagsfeld | 5079-4997 calBCE | Germany | 51.8900000000000 | 11.0400000000000 | 667120 | 406494 | 3725 | 63 | 891477 | 615905 | .. | 0.194 | N1a1a1a2 | 0.992 | [ 0.9880842,0.9952894 ] | 67 | 5663851 | 5114691 | 2855399 | 342222 | 0.115 | 641 | 614 | 0.55 | 0.87 | 66 | passed | 90 | .. S0494 | I0413 | Troc7 | Adelaide | plus | 8 | Spain_EN | Els_Trocs | 5177-5068 calBCE | Spain | 42.5000000000000 | 0.5000000000000 | 836 | 116 | 1 | 51 | 263757 | 190883 | 583 | 0.016 | V | 1.000 | [ 0.9967428,0.9999728 ] | 84 | 9850456 | 8412867 | 6077777 | 1370201 | 0.030 | 1483 | 1 | 0.83 | 3.48 | 56 | passed | 516 | .. S0491 | I0410 | Troc3 | Adelaide | plus | 8 | Spain_EN | Els_Trocs | 5178-5066 calBCE | Spain | 42.5000000000000 | 0.5000000000000 | 2270 | 848 | 14 | 65 | 284615 | 178972 | 347 | 0.017 | pre-T2c1d2 | 0.992 | [ 0.9873560,0.9945048 ] | 99 | 9185882 | 8187153 | 6415946 | 1358368 | 0.030 | 1172 | 1176 | 0.84 | 3.45 | 75 | passed | 113 | .. S0046 | I0046 | HAL5 | Adelaide | plus | 2 | LBK_EN | Halberstadt-Sonntagsfeld | 5206-5004 calBCE | Germany | 51.8900000000000 | 11.0400000000000 | 10060573 | 1824449 | 25345 | 89 | 31191 | 26508 | 82.1 | 0.007 | T2c1d'e'f | 0.993 | [ 0.9870320,0.9967478 ] | 99 | 3940164 | 3422305 | 2811706 | 693648 | 0.018 | 1372 | 1 | 0.75 | 1.76 | 115 | passed | 283 | .. S0809 | I0046 | HAL5 | Adelaide | half | 11 | LBK_EN | Halberstadt-Sonntagsfeld | 5206-5004 calBCE | Germany | 51.9000000000000 | 11.0500000000000 | 497583 | 172218 | 1721 | 64 | 743784 | 479819 | 236 | 0.081 | T2c1d'e'f | 0.993 | [ 0.9890283,0.9949811 ] | 78 | 7093596 | 4440715 | 1656836 | 370529 | 0.063 | 1030 | 1 | 0.56 | 0.94 | 60 | passed | 68 | .. S0048 | I0048 | HAL25 | Adelaide | plus | 2 | LBK_EN | Halberstadt-Sonntagsfeld | 5206-5052 calBCE | Germany | 51.8900000000000 | 11.0400000000000 | 2599 | 167 | 3 | 57 | 80703 | 64040 | 129 | 0.006 | K1a | 0.994 | [ 0.9884414,0.9962785 ] | 77 | 2490052 | 1919907 | 1716000 | 187683 | 0.030 | 398 | 401 | 0.36 | 0.48 | 75 | passed | 597 | .. S0225 | I0056 | HAL14 | Adelaide | plus | 5 | LBK_EN | Halberstadt-Sonntagsfeld | 5206-5052 calBCE | Germany | 51.8900000000000 | 11.0400000000000 | 18456 | 969 | 11 | 27 | 79840 | 51819 | 127 | 0.012 | T2b(8) | 0.839 | [ 0.8098161,0.8725745 ] | 79 | 2256182 | 1777541 | 1650496 | 217324 | 0.029 | 410 | 374 | 0.39 | 0.55 | 87 | passed | 1227 | Manual examination of the mt-DNA reads reveals no evidence of contamination. The samples has two heteroplasmic sites (np 3338 C/T and 16093 C/T), which might expaling the signal of contamination by the contamination estimator, especially since 16093 is well known to be a recurrent mutation polymorphic in humans.. S0226 | I0057 | HAL34 | Adelaide | plus | 5 | LBK_EN | Halberstadt-Sonntagsfeld | 5207-5067 calBCE | Germany | 51.8900000000000 | 11.0400000000000 | 13740 | 437 | 2 | 25 | 82779 | 46573 | 60.7 | 0.008 | N1a1a1 | 1.000 | [ 0.9981528,0.9999876 ] | 54 | 3125419 | 1967967 | 1608404 | 76785 | 0.033 | 307 | 1 | 0.16 | 0.19 | 55 | passed | 3535 | .. S0795 | I0795 | KAR6 | Adelaide | half | 11 | LBK_EN | Karsdorf | 5207-5070 calBCE | Germany | 51.2730000000000 | 11.6559000000000 | 884231 | 90442 | 764 | 53 | 536561 | 370568 | 151 | 0.092 | H1 | 0.982 | [ 0.9749722,0.9867929 ] | 63 | 2031518 | 1043356 | 553314 | 62268 | 0.080 | 111 | 121 | 0.14 | 0.16 | 55 | passed | 315 | .. S0223 | I0054 | UWS4 | Adelaide | plus | 5 | LBK_EN | Unterwiederstedt | 5209-5070 calBCE | Germany | 51.6600000000000 | 11.5300000000000 | 9811238 | 5125780 | 57082 | 66 | 80566 | 52013 | 172 | 0.012 | J1c17 | 0.980 | [ 0.9751038,0.9845945 ] | 70 | 77690446 | 72051450 | 53654665 | 13912076 | 0.023 | 1794 | 2 | 0.98 | 35.33 | 71 | passed | 119 | .. S0397 | I0054 | UWS4 | Adelaide | plus | 7 | LBK_EN | Unterwiederstedt | 5209-5070 calBCE | Germany | 51.6600000000000 | 11.5300000000000 | 1464082 | 805676 | 9384 | 69 | 136935 | 99484 | 331 | 0.006 | J1c17 | 0.953 | [ 0.9061218,0.9754461 ] | 84 | 31043539 | 27763420 | 17704464 | 5601329 | 0.023 | 1790 | 3 | 0.98 | 14.22 | 69 | passed | 89 | .. S0483 | I0176 | SZEH4 | Adelaide | plus | 8 | LBKT_EN | Szemely-Hegyes | 5210-4940 calBCE | Hungary | 46.4000000000000 | 18.7400000000000 | 25605 | 937 | 10 | 63 | 182088 | 115858 | 27.7 | 0.015 | N1a1a1a3 | 1.000 | [ 0.9987014,0.9999886 ] | 59 | 5421708 | 4218205 | 3426906 | 46339 | 0.038 | 143 | 0 | 0.09 | 0.12 | 65 | passed | 1618 | .. S0493 | I0412 | Troc5 | Adelaide | plus | 8 | Spain_EN | Els_Trocs | 5310-5206 calBCE | Spain | 42.5000000000000 | 0.5000000000000 | 45289 | 28322 | 240 | 58 | 328339 | 180994 | 557 | 0.027 | N1a1a1 | 0.991 | [ 0.9867532,0.9944337 ] | 86 | 33076655 | 30261276 | 21447813 | 7281837 | 0.047 | 1513 | 1564 | 0.92 | 18.49 | 64 | passed | 122 | .. S0664 | I0412 | Troc5 | Adelaide | half | 10 | Spain_EN | Els_Trocs | 5310-5206 calBCE | Spain | 42.5000000000000 | 0.5000000000000 | n/a | n/a | n/a | n/a | 1803701 | 769867 | 822 | 0.099 | N1a1a1 | 0.996 | [ 0.9921254,0.9976019 ] | 96 | 23045728 | 19390956 | 8072619 | 2437009 | 0.135 | 1321 | 1352 | 0.88 | 6.19 | 51 | passed | n/a | .. S0665 | I0412 | Troc5 | Adelaide | half | 10 | Spain_EN | Els_Trocs | 5310-5206 calBCE | Spain | 42.5000000000000 | 0.5000000000000 | n/a | n/a | n/a | n/a | 1117353 | 488735 | 687 | 0.104 | N1a1a1 | 0.996 | [ 0.9925749,0.9976539 ] | 91 | 19499919 | 16232552 | 6808858 | 2364469 | 0.135 | 1330 | 1356 | 0.88 | 6.00 | 51 | passed | n/a | .. S0490 | I0409 | Troc1 | Adelaide | plus | 8 | Spain_EN | Els_Trocs | 5311-5218 calBCE | Spain | 42.5000000000000 | 0.5000000000000 | 2097 | 208 | 1 | 74 | 196509 | 144507 | 511 | 0.018 | J1c3 | 1.000 | [ 0.9987404,0.9999893 ] | 106 | 4432026 | 3732670 | 3290513 | 312802 | 0.038 | 831 | 1 | 0.49 | 0.79 | 86 | passed | 1557 | .. S0022_L2 | I0022 | LBK1976 | Boston | half | 14 | LBK_EN | Viesenhaeuser_Hof,_Stuttgart-Muehlhausen | 5500-4800 BCE | Germany | 48.7800000000000 | 9.1800000000000 | 748611 | 350525 | 612 | 57 | 748611 | 333605 | 324 | 0.141 | T2e | 0.994 | [ 0.9892829,0.9960798 ] | 69 | 3274467 | 1758264 | 1147529 | 291015 | 0.207 | 830 | 0 | 0.47 | 0.74 | 45 | passed | 429 | .. S0025_L2 | I0025 | LBK1992 | Boston | half | 14 | LBK_EN | Viesenhaeuser_Hof,_Stuttgart-Muehlhausen | 5500-4800 BCE | Germany | 48.7800000000000 | 9.1800000000000 | 807031 | 656618 | 5707 | 52 | 807031 | 450043 | 828 | 0.171 | T2b | 0.999 | [ 0.9960670,0.9995871 ] | 81 | 5130958 | 4766908 | 2735501 | 1665389 | 0.183 | 1606 | 3 | 0.87 | 4.23 | 55 | passed | 75 | .. S0026_L2 | I0026 | LBK2155 | Boston | half | 14 | LBK_EN | Viesenhaeuser_Hof,_Stuttgart-Muehlhausen | 5500-4800 BCE | Germany | 48.7800000000000 | 9.1800000000000 | 788428 | 618996 | 8502 | 49 | 788428 | 382634 | 669 | 0.163 | T2b | 0.999 | [ 0.9958209,0.9997483 ] | 70 | 6414636 | 5630729 | 3105387 | 2186091 | 0.154 | 1662 | 1 | 0.89 | 5.55 | 51 | passed | 45 | .. S0481 | I0174 | BAM25 | Adelaide | plus | 8 | Starcevo_EN | Alsonyek-Bataszek,_Mernoki_telep | 5710-5530 calBCE | Hungary | 46.2000000000000 | 18.7000000000000 | 36176 | 2528 | 30 | 72 | 202749 | 143587 | 172 | 0.013 | N1a1a1 | 0.999 | [ 0.9967456,0.9996938 ] | 80 | 6894689 | 5953426 | 5053196 | 152212 | 0.034 | 282 | 282 | 0.29 | 0.39 | 77 | passed | 884 | .. S0011 | I0011 | Motala1 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | n/a | n/a | n/a | n/a | 187740 | 82298 | 239 | 0.007 | U5a1 | 0.995 | [ 0.9913702,0.9970486 ] | 79 | 6061308 | 2337806 | 2221410 | 570943 | 0.017 | 1091 | 3 | 0.65 | 1.45 | 81 | passed | n/a | .. S0012 | I0012 | Motala2 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | 3339 | 132 | 1 | 67 | 181462 | 101859 | 347 | 0.008 | U2e1 | 0.997 | [ 0.9946402,0.9987111 ] | 83 | 13513744 | 5843149 | 5133352 | 1149590 | 0.014 | 1151 | 1225 | 0.83 | 2.92 | 78 | passed | 1268 | .. S0013 | I0013 | Motala3 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | n/a | n/a | n/a | n/a | 163637 | 68129 | 235 | 0.007 | U5a1 | 0.967 | [ 0.9595028,0.9726388 ] | 87 | 10834268 | 3227173 | 3229809 | 784709 | 0.014 | 898 | 977 | 0.71 | 1.99 | 92 | passed | n/a | .. S0014 | I0014 | Motala4 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | n/a | n/a | n/a | n/a | 144589 | 62134 | 228 | 0.009 | U5a2d | 0.991 | [ 0.9845365,0.9943545 ] | 82 | 29160790 | 9804807 | 9257499 | 2317303 | 0.016 | 1581 | 3 | 0.87 | 5.88 | 82 | passed | n/a | .. S0015 | I0015 | Motala6 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | n/a | n/a | n/a | n/a | 152429 | 59435 | 241 | 0.010 | U5a2d | 0.994 | [ 0.9899754,0.9961715 ] | 92 | 20697782 | 5479581 | 5534463 | 1403599 | 0.016 | 1173 | 1252 | 0.80 | 3.56 | 93 | passed | n/a | .. S0016 | I0016 | Motala9 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | n/a | n/a | n/a | n/a | 166884 | 72658 | 245 | 0.007 | U5a2 | 0.980 | [ 0.9748690,0.9854657 ] | 82 | 19300421 | 5564832 | 5471461 | 972641 | 0.009 | 1057 | 1145 | 0.78 | 2.47 | 81 | passed | n/a | .. S0017 | I0017 | Motala12 | Tuebingen | plus | 12 | Motala_HG | Motala | 5898-5531 calBCE | Sweden | 58.5350000000000 | 15.0460000000000 | 2675 | 238 | 0 | 64 | 152253 | 78610 | 292 | 0.005 | U2e1 | 0.989 | [ 0.9851613,0.9924840 ] | 85 | 48796250 | 20701235 | 16532891 | 3658825 | 0.014 | 1621 | 1725 | 0.95 | 9.29 | 74 | passed | n/a | .. S0230 | I0061 | UzOO74 | Adelaide | plus | 5 | Karelia_HG | Yuzhnyy_Oleni_Ostrov,_Karelia | 5500-5000 BCE | Russia | 61.6500000000000 | 35.6500000000000 | 9048388 | 3549900 | 36296 | 63 | 192580 | 138345 | 366.0 | 0.011 | C1g | 0.995 | [ 0.9915251,0.9974554 ] | 75 | 16660129 | 15907089 | 13478961 | 2827934 | 0.015 | 1614 | 1671 | 0.95 | 7.18 | 72 | passed | 202 | .. S0670 | I0061 | UzOO74 | Adelaide | half | 10 | Karelia_HG | Yuzhnyy_Oleni_Ostrov,_Karelia | 5500-5000 BCE | Russia | 61.6500000000000 | 35.6500000000000 | n/a | n/a | n/a | n/a | 1467589 | 905344 | 637.0 | 0.092 | C1g | 0.996 | [ 0.9931726,0.9980843 ] | 79 | 2743246 | 2275503 | 1168312 | 523288 | 0.062 | 863 | 819 | 0.63 | 1.33 | 57 | passed | n/a | ..