Y-SNP calls for Damgaard (2018) 137 ancient human genomes from the Eurasian…

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      Carlos Quiles
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      Damgaard, P.d.B., Marchi, N., Rasmussen, S. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018).

      https://doi.org/10.1038/s41586-018-0094-2

      Abstract:

      For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth–fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.

      Accession number: PRJEB23635

      Batch Y-chromosome SNP Calls with Yleaf v. 2.3 from FASTQ files, bwa-mem with hg38 reference, and parameters r=1, q=0, b=0.

      Google Drive.

      Haplogroup.info.

      The following is a list of automated Y-DNA haplogroup predictions obtained with Clean tree v2:

      WARNING: Please note that the haplogroup prediction algorithm works best with modern DNA, and its strict requirements make the prediction rather impractical for ancient DNA – in fact, males usually turn out to have not enough quality for a reliable prediction.

      If anything, positive haplogroup predictions (especially under R1b and I2) will normally turn out to be wrong because they are based on few reads, due to the sample being either a) female or b) low coverage.

      The usual process for checking out Y-chromosome haplogroups in ancient DNA samples is as follows:

      1. Select the male individual you want to check out for in the Ancient DNA Dataset.
      2. Look up its library ID (object-ID) at ENA Browser search form (top right) to obtain the accession number(s) for the available sample(s) corresponding to that individual.
      3. Look for files obtained with Yleaf for that accession number(s); more specifically, look for individual Derived and Ancestral SNPs in the ACCESSION_NUMBER.out or ACCESSION_NUMBER.out.csv documents.

      When in doubt about a specific sample, you can ask a question in this thread.

      ERR2505977 N1a1a1a1a N-CTS12907*(xA14014,Y15814,Y20922,M2036) 170411 472 1.0 1.0 1.0 1.0
      ERR2505926 Q1b1a~ Q-CTS7619*(xCTS11969,Z19276,Y5267) 3763723 18894 1.0 1.0 1.0 1.0
      ERR2505969 NA NA 1769151 9077 0.0 0.0 1.0 1.0
      ERR2505919 NA NA 133516 138 0 0 0 0
      ERR2505883 NA NA 221767 84 0 0 0 0
      ERR2505899 NA NA 3997267 20825 0.0 0.0 1.0 1.0
      ERR2505922 NA NA 5891233 30158 0.0 0.0 1.0 1.0
      ERR2505914 NA NA 4110534 21431 0.0 0.0 1.0 1.0
      ERR2505856 NA NA 95160 19 0 0 0 0
      ERR2505934 NA NA 124375 120 0 0 0 0
      ERR2505881 NA NA 5693326 28798 0.0 0.0 1.0 1.0
      ERR2505864 NA NA 5948741 30043 0.0 0.0 1.0 1.0
      ERR2505852 NA NA 139119 31 0 0 0 0
      ERR2505933 NA NA 7765378 41941 0.0 0.0 1.0 1.0
      ERR2505845 NA NA 10947468 54917 0.0 0.0 1.0 1.0
      ERR2505935 NA NA 3519754 20491 0 0 0 0
      ERR2505936 NA NA 7320899 38519 0.0 0.0 1.0 0.0
      ERR2505847 NA NA 3414298 17546 0.0 0.0 1.0 1.0
      ERR2505920 NA NA 8232081 42281 0.0 0.0 1.0 1.0
      ERR2505909 NA NA 9777798 50085 0.0 0.0 1.0 1.0
      ERR2505882 N1a1a1a1a1a1a1 N-B215*(xY13977,Y28546,Y20413,Y17694,Y13479,Y18701,Y9018,Z35039) 973029 4749 1.0 1.0 1.0 1.0
      ERR2505950 J2a1a1b3 J-Z396/etc 4907185 25223 1.0 1.0 1.0 1.0
      ERR2505863 NA NA 106850 25 0 0 0 0
      ERR2505895 NA NA 91172 25 0 0 0 0
      ERR2505850 NA NA 4741278 24468 0.0 0.0 1.0 1.0
      ERR2505967 NA NA 8063124 41491 0 0 0 0
      ERR2505877 NA NA 103906 71 0 0 0 0
      ERR2505865 R1a1a~ R-CTS1619*(xCTS7288,FGC10002,FGC2634,Y4459,YP270,YP5311,FGC19245,Y17526,YP4827,YP5198,Y35750,Y30194,YP1078,Y3842,YP4659,FGC21240,Y4376,Y17987,BY32485,A15622,PH4687,FGC74372,FGC4539,FGC15009,S5148,YP1427,FGC25763,YP4454,YP4252,YP5689,YP4476,Y29906,M11362,YP6464,YP5860,FGC40642,YP1199,YP5236,FGC28696,BY11599,YP4122,YP712,YP5882,FGC64143,YP5974,AM00480,YP4912,Y37794,YP4975,Y19841,YP522,FGC59420,M12301,FGC48782,YP1710,YP1353,S10885,Y38014,FGC113,Y58,Y28653,FGC30895,Y20792,Y35117,YP5591,YP1061) 648435 3577 1.0 1.0 1.0 1.0
      ERR2505896 NA NA 2916285 15081 0.0 0.0 1.0 1.0
      ERR2505849 NA NA 106709 23 0 0 0 0
      ERR2505944 NA NA 2903828 15393 0.0 0.0 1.0 1.0
      ERR2505918 NA NA 9863713 52002 0.0 0.0 1.0 1.0
      ERR2505900 NA NA 5437025 28207 0 0 0 0
      ERR2505943 R1a1a~ R-F1050/etc*(xM637,YP1050) 4294801 22420 1.0 1.0 1.0 1.0
      ERR2505959 NA NA 130598 53 0 0 0 0
      ERR2505851 NA NA 83018 33 0 0 0 0
      ERR2505875 NA NA 114228 47 0 0 0 0
      ERR2505905 Q1b1a3a~ Q-YP779*(xY12110) 3263848 16819 1.0 1.0 1.0 1.0
      ERR2505912 NA NA 164868 101 0.0 0.0 1.0 1.0
      ERR2505890 NA NA 136808 72 0 0 0 0
      ERR2505979 NA NA 152106 94 0 0 0 0
      ERR2505931 NA NA 9163409 46225 0.0 0.0 1.0 0.0
      ERR2505898 NA NA 78108 37 0 0 0 0
      ERR2505957 NA NA 154168 69 0 0 0 0
      ERR2505972 NA NA 2354815 11645 0.0 1.0 1.0 0.0
      ERR2505873 R1a1a1b2a2a1d3~ R-Y37794 1139022 5957 1.0 1.0 1.0 1.0
      ERR2505867 NA NA 128288 52 0 0 0 0
      ERR2505938 NA NA 6264162 34219 0.0 0.0 1.0 1.0
      ERR2505964 NA NA 179316 137 0 0 0 0
      ERR2505955 NA NA 73222 239 0 0 0 0
      ERR2505949 NA NA 5496680 27986 0.0 0.0 1.0 1.0
      ERR2505911 NA NA 97008 44 0 0 0 0
      ERR2505963 R1a1a1b~ R-CTS5508*(xAM01874,S446,S3358,Y10806,FGC11882,Y17491,YP5970,M648,FGC7398,FGC7400,FGC57581,S24826,Y34245,Y34257,YP6238,Y34219,Y35106,YP5560,Y2436,Z29115,F24353,Y2428,SUR1,YP1709,S23592,CTS3412,FGC122,YP5937,Y19610,YP641,Y53,M12222,YP4869,CTS2887,YP5322,YP1506,Y20787,Y34292,YP5597) 3501486 17931 1.0 1.0 1.0 1.0
      ERR2505897 NA NA 69012 23 0 0 0 0
      ERR2505857 NA NA 108773 29 0 0 0 0
      ERR2505862 Q2b2~ Q-YP4497/etc*(xY6057) 3162479 16195 1.0 1.0 1.0 1.0
      ERR2505928 Q1b1a3b Q-Y11939/etc*(xF1508,Y12676) 2708456 13838 1.0 1.0 1.0 1.0
      ERR2505858 NA NA 300594 1018 0 0 0 0
      ERR2505861 NA NA 1626478 8472 0.0 0.0 1.0 1.0
      ERR2505902 NA NA 8486882 42591 0.0 0.0 1.0 1.0
      ERR2505932 NA NA 286770 208 0 0 0 0
      ERR2505921 NA NA 11331837 56552 0 0 0 0
      ERR2505854 NA NA 166341 42 0 0 0 0
      ERR2505940 NA NA 2261374 11800 0.0 0.0 1.0 1.0
      ERR2505892 NA NA 130239 54 0 0 0 0
      ERR2505973 NA NA 7206642 36480 0.0 0.0 1.0 1.0
      ERR2505885 NA NA 1835555 9192 0.0 0.0 1.0 1.0
      ERR2505903 R1a1a1~ R-CTS11913*(xYP681,YP1133,YP551,S2862,S2880,YP1014,YP6477,Y22236,Y16274,Y20982,YP414,YP5297,Y37289,YP5248,V1632,YP270,FGC46022,YP5222,FGC19231,YP5936,YP4843,Y17530,Y21042,Y35771,FGC39322,FGC21234,FGC37071,Y36,FGC15009,FGC11882,YP5874,Y908,FGC7402,M12369,YP5544,Y933,Y20652,YP6360,YP529,YP5277,YP1344,FGC56425,FGC110,YP635,YP5645) 451655 2480 1.0 1.0 1.0 1.0
      ERR2505894 NA NA 3858057 19678 0 0 0 0
      ERR2505907 NA NA 10136395 51155 0.0 0.0 1.0 1.0
      ERR2505901 NA NA 134630 156 0 0 0 0
      ERR2505859 NA NA 1714244 9213 0.0 0.0 1.0 1.0
      ERR2505961 Q1b1a3a1~ Q-YP762/etc*(xL329,BZ427) 3733372 19071 1.0 1.0 1.0 1.0
      ERR2505947 NA NA 3782101 20040 0.0 0.0 1.0 1.0
      ERR2505872 NA NA 2020632 10719 0.0 0.0 1.0 1.0
      ERR2505887 R1b1a1b R-CTS8052/etc*(xA560,DF95,S15627,A8558,L188,FGC31485,L671,CTS7193.2,M222,S775,FGC5589,Y11640,BY2634,Z17823,Z21253,Z16377,FGC11803,ZS4590,A6534,FGC5626,Z2186,FGC36536,Y16765,Y16288,S6166,FGC3903,S5488,FGC33393,PF3434.1,A92,A7811,FGC37095,PF7558) 175341 1047 1.0 1.0 1.0 1.0
      ERR2505952 R1a R-L146*(xS2848,AM01875,S204,FGC11882,Y17491,YP5967,AM00484,SUR2,M12319,FGC48792,Y29561,Y12480,S15948,F1345,Y2169,Y37,FGC30910,CTS2887,YP1451,YP5323,YP1507,Y20793,Y34298,Y24737,YP1050,GG062.2,YP4173) 3120882 15773 1.0 1.0 1.0 1.0
      ERR2505946 Q1a2a1~ Q-YP813/etc*(xBZ660) 1255542 6695 1.0 1.0 1.0 1.0
      ERR2505966 NA NA 51586 42 0 0 0 0
      ERR2505924 NA NA 5019453 28930 0 0 0 0
      ERR2505904 NA NA 446580 2241 0.0 0.0 1.0 1.0
      ERR2505868 R1a1a1b2a2a3~ R-YP349/etc*(xFGC48792,Y29561,S23201) 7494399 38223 1.0 1.0 1.0 1.0
      ERR2505853 NA NA 6064292 31375 0 0 0 0
      ERR2505916 NA NA 172503 381 0 0 0 0
      ERR2505930 Q1b1b~ Q-FGC2592/etc*(xYP4015) 3555228 18310 1.0 1.0 1.0 1.0
      ERR2505915 NA NA 6587061 34047 0.0 0.0 1.0 1.0
      ERR2505951 NA NA 4161436 21311 0 0 0 0
      ERR2505954 NA NA 111050 120 0 0 0 0
      ERR2505906 NA NA 2714585 13816 0.0 1.0 1.0 0.0
      ERR2505908 NA NA 10908374 54398 0.0 0.0 1.0 1.0
      ERR2505927 Q1b1~ Q-M1178/etc*(xCTS11969,M971,Y5261,YP4048) 1093805 5735 1.0 1.0 1.0 1.0
      ERR2505939 R1a1a1~ R-M782*(xS2846,PF7525,S205,CTS1211,YP5316,YP5543,YP4901,BY27380,Y32866,CTS3802,FGC36400,YP1393,YP5007,YP4876,Y32869,YP4473,YP994,CTS8401,S6242,YP6458,YP5865,Y36450,YP403,Z1662,FGC28673,YP1179,YP1373,YP3897,YP698,Y31834,FGC64142,YP5975,AM00480,Y48,YP4912,YP6321,FGC10235,FGC22475,Y36348,YP6331,Y15121,YP1556,YP1347,S22857,Y38022,S3406,M12210,FGC126,YP4770,Y58,CTS9094,YP5321,YP5589) 876541 5060 1.0 1.0 1.0 1.0
      ERR2505956 NA NA 140222 45 0 0 0 0
      ERR2505884 NA NA 4422 4 0 0 0 0
      ERR2505913 NA NA 9860158 49981 0.0 0.0 1.0 1.0
      ERR2505976 NA NA 5349333 26747 0.0 0.0 1.0 1.0
      ERR2505860 NA NA 1399846 7331 0 0 0 0
      ERR2505917 NA NA 8891147 44901 0.0 0.0 1.0 0.0
      ERR2505889 G2a1a1 G-FGC684*(xY110246.2,Z45050,Z44788,FGC1125,BY187066,Z25119.2,FGC65335) 389530 2348 1.0 1.0 1.0 1.0
      ERR2505970 NA NA 2223646 11741 0.0 0.0 1.0 1.0
      ERR2505941 NA NA 4610475 23157 0.0 0.0 1.0 1.0
      ERR2505953 NA NA 1684434 9114 0 0 0 0
      ERR2505855 R1b1a1 R-CTS5577/etc*(xY13878,L150.1) 4188792 21782 1.0 1.0 1.0 1.0
      ERR2505891 NA NA 121503 30 0 0 0 0
      ERR2505846 NA NA 166103 177 0 0 0 0
      ERR2505886 NA NA 218743 1270 0 0 0 0
      ERR2505925 NA NA 2049661 10750 0.0 0.0 1.0 1.0
      ERR2505848 NA NA 3974980 20420 0 0 0 0
      ERR2505878 NA NA 854788 4484 0 0 0 0
      ERR2505962 NA NA 5016111 25843 0.0 0.0 1.0 1.0
      ERR2505945 NA NA 89205 72 0 0 0 0
      ERR2505870 NA NA 6264257 31734 0.0 0.0 1.0 1.0
      ERR2505923 NA NA 5847238 29815 0.0 0.0 1.0 1.0
      ERR2505876 R1a1a1b2a2a3b~ R-YP1710*(xYP1555) 1646055 8565 1.0 1.0 1.0 1.0
      ERR2592344 NA NA 2155676 11713 0.0 0.0 1.0 1.0
      ERR2505942 NA NA 131323 32 0 0 0 0
      ERR2505879 NA NA 8900391 44642 0.0 0.0 1.0 1.0
      ERR2505888 NA NA 77194 48 0 0 0 0
      ERR2505971 NA NA 208615 109 0 0 0 0
      ERR2505975 NA NA 8472239 42576 0 0 0 0
      ERR2505965 NA NA 8365413 43566 0 0 0 0
      ERR2505978 NA NA 159907 66 0 0 0 0
      ERR2505893 R1a1a1b~ R-F3044*(xAM01874,CTS456,CTS3402,YP1155,CTS11934,S5293,YP5158,YP6454,YP403,YP594,FGC28656,YP1375,YP3912,Y24038,YP5872,FGC64144,YP5961,F992) 3051206 15705 1.0 1.0 1.0 1.0
      ERR2505960 R1b2 R-BY14357*(xM335,SK2055) 261145 507 1.0 1.0 1.0 1.0
      ERR2505929 NA NA 234969 266 0 0 0 0
      ERR2505880 NA NA 142810 61 0 0 0 0
      ERR2505869 NA NA 2862020 15017 0.0 0.0 1.0 1.0
      ERR2505974 NA NA 1828311 9475 0.0 0.0 1.0 1.0
      ERR2505874 NA NA 44001 30 0 0 0 0
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