If there are studies with data that hasnt been converted to G25 provide them here

[ilabv]

How about this one? Red Deer Cave
https://www.cell.com/current-biology/ful...22)00928-9

I checked that once, the SNP count was pitiful
And going through the Chinese database was awful too.

They claim to have "∼0.113× coverage of the nuclear genome"

It's not great but should be enough I'd think?

[teepean]

I've never seen those, LUN004 and BAL003.

https://journals.plos.org/plosgenetics/a...en.1010360

I created the dataset about a year ago:

https://drive.google.com/drive/folders/1...sp=sharing

Unfortunately, not enough data for the G25

I am not sure what I used previously as a source but here they are.

Code:

Scaled

Pict:BAL003.merged,0.12862,0.133034,0.062979,0.049742,0.040623,0.020638,0.00047,0.000231,0.004909,0.010752,-0.008444,0.003897,-0.021407,-0.014175,0.020629,0.005171,-0.005737,-0.003674,0.002137,0.003377,0.008735,0.004204,-0.003697,0.002651,0.003832
Pict:LUN004.merged,0.134311,0.12491,0.064111,0.044897,0.040315,0.008088,0.003525,0.002077,0.007772,0.007472,-0.012991,0.010341,-0.01888,-0.015414,0.020494,-0.005304,-0.022556,0.002787,0.004399,-0.00963,0.00574,-0.001113,-0.00949,0.003976,-0.003712

Raw

Pict:BAL003.merged,0.0113,0.0131,0.0167,0.0154,0.0132,0.0074,0.0002,0.0001,0.0024,0.0059,-0.0052,0.0026,-0.0144,-0.0103,0.0152,0.0039,-0.0044,-0.0029,0.0017,0.0027,0.007,0.0034,-0.003,0.0022,0.0032
Pict:LUN004.merged,0.0118,0.0123,0.017,0.0139,0.0131,0.0029,0.0015,0.0009,0.0038,0.0041,-0.008,0.0069,-0.0127,-0.0112,0.0151,-0.004,-0.0173,0.0022,0.0035,-0.0077,0.0046,-0.0009,-0.0077,0.0033,-0.0031

[Norfern-Ostrobothnian]

My guess is that you accidentally used one of the .bam files instead of the merged .cram files for the samples.

[crashdoc]

How about this one? Red Deer Cave
https://www.cell.com/current-biology/ful...22)00928-9

I checked that once, the SNP count was pitiful
And going through the Chinese database was awful too.

They claim to have "∼0.113× coverage of the nuclear genome"

It's not great but should be enough I'd think?

~63k snps on the 1240k set, not enough for G25

[Bukva_]

Network of large pedigrees reveals social practices of Avar communities

https://www.ebi.ac.uk/ena/browser/view/PRJEB72021

[ilabv]

Network of large pedigrees reveals social practices of Avar communities

https://www.ebi.ac.uk/ena/browser/view/PRJEB72021

Have these really been available for a month and no one has done them?

[Bukva_]

Network of large pedigrees reveals social practices of Avar communities

https://www.ebi.ac.uk/ena/browser/view/PRJEB72021

Have these really been available for a month and no one has done them?

As far as I know, no. I asked in Stolarek thread also, so we will see.

[ilabv]

Network of large pedigrees reveals social practices of Avar communities

https://www.ebi.ac.uk/ena/browser/view/PRJEB72021

Have these really been available for a month and no one has done them?

As far as I know, no. I asked in Stolarek thread also, so we will see.

Yes, let me know if its needed. Thanks

[Bukva_]

Network of large pedigrees reveals social practices of Avar communities

https://www.ebi.ac.uk/ena/browser/view/PRJEB72021

Have these really been available for a month and no one has done them?

As far as I know, no. I asked in Stolarek thread also, so we will see.

Yes, let me know if its needed. Thanks

No one responded, so I guess no. You can send them.

[G-Man]

First ancient DNA analysis of mummies from the post-Scythian Oglakhty cemetery in South Siberia  https://doi.org/10.21203/rs.3.rs-1993191/v1

Raw data  https://www.ebi.ac.uk/ena/browser/view/PRJNA872874

[ilabv]

There have been many papers without G25 coordinates (recently and perhaps older ones too).

If you know of any studies which dont have G25 coordinates please send me their raw data or at least the study they come from. Teepean has been helping me so I can help the community gong forward

https://www.sciencedirect.com/science/ar...4223022927

https://www.sciencedirect.com/science/ar...4223011112

Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps (all 20 samples converted below):

Scaled

Italy:1895,0.122929,0.15436,0.044123,-0.001292,0.044008,0.004462,-0.00329,0.009,0.00859,0.023873,-0.005846,0.009442,-0.00223,-0.012937,0.001357,0.009546,0.008605,-0.000633,0.009679,0.005127,-0.003244,0.01014,-0.000739,0.010001,0.002994
Italy:2067,0.130897,0.151314,0.003771,-0.009044,0.025543,-0.006972,0.008225,0.006,0.010431,0.028247,-0.002273,-0.002098,-0.01665,-0.009221,-0.01045,0.000265,0.001304,-0.00266,-0.00176,-0.007379,0.002995,0.003957,0.008627,-0.003615,-0.007065
Italy:2068,0.120652,0.148267,0.0445,-0.01292,0.049855,-0.004462,0.004935,0.003231,0.019634,0.026789,-0.002923,0.00015,-0.012042,-0.003165,-0.017644,0.011933,0.02373,0.00228,0.006536,-0.008004,0.001373,-0.00643,0.000986,-0.00253,-0.009101
Italy:2069,0.124067,0.158423,0.026021,-0.016473,0.03416,-0.008646,0.000235,-0.001154,0.005113,0.031162,-0.00682,0.009292,-0.016501,-0.00578,-0.010179,0.005967,0.022035,0.005954,-0.004777,0.000125,-0.001872,0.006677,0.000986,0.002651,-0.00455
Italy:2324,0.111547,0.142174,0.044123,0.014212,0.044008,-0.003347,0.003995,0.003,0.005318,0.015308,-0.011205,0.003147,-0.014717,-0.00523,-0.001493,0.008088,0.001565,0.011655,0.006285,0.003627,0.004866,0.008161,-0.004683,0.004579,-0.005269
Italy:2404,0.120652,0.149283,0.033941,-0.018411,0.045239,-0.01506,-0.00376,-0.013153,0.020657,0.032074,-0.003085,0.008093,-0.016055,-0.007019,0.004072,0.012198,0.008605,0.005321,0.004399,0.002251,-0.003494,-0.002102,-0.000616,-0.003856,-0.005508
Italy:2405,0.120652,0.155376,0.033187,-0.009367,0.056318,-0.008367,-0.00376,-0.003461,0.010226,0.032438,-0.003573,0.007194,-0.022448,-0.003716,-0.009908,0.000133,0.016559,-0.005448,0,0.003752,0.00287,0.011871,-0.008751,0.000361,-0.007185
Italy:2417,0.125205,0.145221,0.058454,0.006137,0.0397,0.003904,0.001175,0.007384,0.015339,0.027882,-0.010393,0.005245,-0.012636,-0.012386,0.009365,0.003978,0.009779,0.002027,0.003268,-0.006753,0.002995,0.011005,-0.002835,0.000723,0.008981
Italy:2418,0.126344,0.14319,0.021873,-0.021641,0.036314,-0.012271,-0.000705,0.004615,0.017794,0.030433,0.004872,0.010191,-0.011001,-0.005505,-0.002714,-0.009149,-0.007041,0.003927,0.006034,-0.003502,0.001996,0.00272,-0.00456,-0.003856,-0.001557
Italy:2419,0.117238,0.146236,0.018856,-0.018734,0.024004,-0.013108,-0.00705,-0.005538,0.013703,0.024966,0.000812,-0.000599,-0.010704,-0.01734,-0.002036,0.007558,0.013169,-0.0019,-0.001508,0.004502,0.000749,0.000989,-0.003328,0.00253,-0.000359
Italy:2422,0.129758,0.137096,0.040352,0.005491,0.036314,0.000558,-0.007285,-0.002077,0.01084,0.017312,0.001299,-0.007493,-0.025867,0.001239,-0.001357,-0.016441,-0.00013,0.0019,0.009679,-0.005628,-0.019965,0.003957,-0.002711,-0.006025,0.00467
Italy:2423,0.126344,0.148267,0.026776,-0.013243,0.039392,-0.005857,-0.003525,0.000462,0.022702,0.032802,0.003573,0.000749,-0.012785,-0.010597,-0.0038,-0.00305,0.004694,0.00038,-0.005782,-0.003377,-0.002995,-0.002226,-0.010723,-0.000964,-0.005868
Italy:2424,0.112685,0.161469,0.018856,-0.020995,0.040007,0.005857,-0.005405,0.00923,0.016975,0.033167,-0.004384,0.008093,-0.013379,-0.010735,-0.011129,-0.012861,-0.015776,0.006714,-0.001885,-0.017133,0.004866,0.01014,0.000493,-0.000482,-0.002155
Italy:2425,0.125205,0.160454,0.044877,-0.000323,0.036314,-0.003068,-0.00705,0.007154,0.009613,0.036994,0.002111,0.005095,-0.026313,0.000826,-0.007329,-0.011535,-0.019166,0.006461,0.004777,-0.007754,0.004492,0.005935,-0.003204,0.004217,-0.000958
Italy:2427,0.12862,0.137096,0.036204,0.003553,0.035699,-0.007809,-0.00517,0.006461,0.023111,0.030251,-0.006171,0.008393,-0.011744,0.011423,-0.003664,-0.020154,-0.013951,-0.0019,0.001508,-0.009379,-0.007487,0.006554,-0.002711,-0.006868,-0.007305
Italy:2428,0.120652,0.148267,0.022627,-0.021318,0.039084,-0.011713,0.001645,-0.001615,0.005318,0.027518,0.005684,0.010641,-0.011596,-0.011285,-0.003936,0.000663,0.00326,-0.000887,-0.001006,0.001251,-0.006239,0.003586,0.000616,0.005784,-0.0097
Italy:2429,0.129758,0.138112,0.047894,-0.003553,0.031698,0.005299,0.005405,-0.000923,-0.005113,0.024602,-0.002761,0.002997,-0.009514,-0.001376,0.007057,-0.004375,-0.006519,0.008615,-0.001257,0.005503,0.002246,0.008656,-0.003574,-0.006386,-0.001557
Italy:2430,0.126344,0.148267,0.043369,0.008398,0.056626,-0.000279,-0.002585,0.000462,0.021884,0.030616,-0.001461,0.012289,-0.013082,-0.009634,-0.003529,-0.004641,0.005085,0.001267,0.000628,-0.010255,-0.00287,-0.00371,-0.001725,-0.003615,0.003353


Raw

Italy:1895,0.0108,0.0152,0.0117,-0.0004,0.0143,0.0016,-0.0014,0.0039,0.0042,0.0131,-0.0036,0.0063,-0.0015,-0.0094,0.001,0.0072,0.0066,-0.0005,0.0077,0.0041,-0.0026,0.0082,-0.0006,0.0083,0.0025
Italy:2067,0.0115,0.0149,0.001,-0.0028,0.0083,-0.0025,0.0035,0.0026,0.0051,0.0155,-0.0014,-0.0014,-0.0112,-0.0067,-0.0077,0.0002,0.001,-0.0021,-0.0014,-0.0059,0.0024,0.0032,0.007,-0.003,-0.0059
Italy:2068,0.0106,0.0146,0.0118,-0.004,0.0162,-0.0016,0.0021,0.0014,0.0096,0.0147,-0.0018,0.0001,-0.0081,-0.0023,-0.013,0.009,0.0182,0.0018,0.0052,-0.0064,0.0011,-0.0052,0.0008,-0.0021,-0.0076
Italy:2069,0.0109,0.0156,0.0069,-0.0051,0.0111,-0.0031,0.0001,-0.0005,0.0025,0.0171,-0.0042,0.0062,-0.0111,-0.0042,-0.0075,0.0045,0.0169,0.0047,-0.0038,0.0001,-0.0015,0.0054,0.0008,0.0022,-0.0038
Italy:2324,0.0098,0.014,0.0117,0.0044,0.0143,-0.0012,0.0017,0.0013,0.0026,0.0084,-0.0069,0.0021,-0.0099,-0.0038,-0.0011,0.0061,0.0012,0.0092,0.005,0.0029,0.0039,0.0066,-0.0038,0.0038,-0.0044
Italy:2404,0.0106,0.0147,0.009,-0.0057,0.0147,-0.0054,-0.0016,-0.0057,0.0101,0.0176,-0.0019,0.0054,-0.0108,-0.0051,0.003,0.0092,0.0066,0.0042,0.0035,0.0018,-0.0028,-0.0017,-0.0005,-0.0032,-0.0046
Italy:2405,0.0106,0.0153,0.0088,-0.0029,0.0183,-0.003,-0.0016,-0.0015,0.005,0.0178,-0.0022,0.0048,-0.0151,-0.0027,-0.0073,0.0001,0.0127,-0.0043,0,0.003,0.0023,0.0096,-0.0071,0.0003,-0.006
Italy:2417,0.011,0.0143,0.0155,0.0019,0.0129,0.0014,0.0005,0.0032,0.0075,0.0153,-0.0064,0.0035,-0.0085,-0.009,0.0069,0.003,0.0075,0.0016,0.0026,-0.0054,0.0024,0.0089,-0.0023,0.0006,0.0075
Italy:2418,0.0111,0.0141,0.0058,-0.0067,0.0118,-0.0044,-0.0003,0.002,0.0087,0.0167,0.003,0.0068,-0.0074,-0.004,-0.002,-0.0069,-0.0054,0.0031,0.0048,-0.0028,0.0016,0.0022,-0.0037,-0.0032,-0.0013
Italy:2419,0.0103,0.0144,0.005,-0.0058,0.0078,-0.0047,-0.003,-0.0024,0.0067,0.0137,0.0005,-0.0004,-0.0072,-0.0126,-0.0015,0.0057,0.0101,-0.0015,-0.0012,0.0036,0.0006,0.0008,-0.0027,0.0021,-0.0003
Italy:2422,0.0114,0.0135,0.0107,0.0017,0.0118,0.0002,-0.0031,-0.0009,0.0053,0.0095,0.0008,-0.005,-0.0174,0.0009,-0.001,-0.0124,-0.0001,0.0015,0.0077,-0.0045,-0.016,0.0032,-0.0022,-0.005,0.0039
Italy:2423,0.0111,0.0146,0.0071,-0.0041,0.0128,-0.0021,-0.0015,0.0002,0.0111,0.018,0.0022,0.0005,-0.0086,-0.0077,-0.0028,-0.0023,0.0036,0.0003,-0.0046,-0.0027,-0.0024,-0.0018,-0.0087,-0.0008,-0.0049
Italy:2424,0.0099,0.0159,0.005,-0.0065,0.013,0.0021,-0.0023,0.004,0.0083,0.0182,-0.0027,0.0054,-0.009,-0.0078,-0.0082,-0.0097,-0.0121,0.0053,-0.0015,-0.0137,0.0039,0.0082,0.0004,-0.0004,-0.0018
Italy:2425,0.011,0.0158,0.0119,-0.0001,0.0118,-0.0011,-0.003,0.0031,0.0047,0.0203,0.0013,0.0034,-0.0177,0.0006,-0.0054,-0.0087,-0.0147,0.0051,0.0038,-0.0062,0.0036,0.0048,-0.0026,0.0035,-0.0008
Italy:2427,0.0113,0.0135,0.0096,0.0011,0.0116,-0.0028,-0.0022,0.0028,0.0113,0.0166,-0.0038,0.0056,-0.0079,0.0083,-0.0027,-0.0152,-0.0107,-0.0015,0.0012,-0.0075,-0.006,0.0053,-0.0022,-0.0057,-0.0061
Italy:2428,0.0106,0.0146,0.006,-0.0066,0.0127,-0.0042,0.0007,-0.0007,0.0026,0.0151,0.0035,0.0071,-0.0078,-0.0082,-0.0029,0.0005,0.0025,-0.0007,-0.0008,0.001,-0.005,0.0029,0.0005,0.0048,-0.0081
Italy:2429,0.0114,0.0136,0.0127,-0.0011,0.0103,0.0019,0.0023,-0.0004,-0.0025,0.0135,-0.0017,0.002,-0.0064,-0.001,0.0052,-0.0033,-0.005,0.0068,-0.001,0.0044,0.0018,0.007,-0.0029,-0.0053,-0.0013
Italy:2430,0.0111,0.0146,0.0115,0.0026,0.0184,-0.0001,-0.0011,0.0002,0.0107,0.0168,-0.0009,0.0082,-0.0088,-0.007,-0.0026,-0.0035,0.0039,0.001,0.0005,-0.0082,-0.0023,-0.003,-0.0014,-0.003,0.0028


If you have any other samples, old or new, you want me to have converted, please send them to me. I'm looking to do every missing sample that doesn't have G25 coordinates (hundreds of Avars, the Basel-Waisenhaus Swiss samples, and both Tashtyk culture samples are on the way)

[Ajeje Brazorf]

Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant’Angelo (Calabria, Italy)

https://www.nature.com/articles/s41598-023-39250-y

[ilabv]

Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant’Angelo (Calabria, Italy)

https://www.nature.com/articles/s41598-023-39250-y

Thank you Ajeje. Keep them coming. I will have SNP counts sent for all samples today or tomorrow

[Ajeje Brazorf]

Archaeogenetic analysis revealed East Eurasian paternal origin to the Aba royal family of Hungary

https://www.biorxiv.org/content/10.1101/...0.585718v1

[Norfern-Ostrobothnian]

First ancient DNA analysis of mummies from the post-Scythian Oglakhty cemetery in South Siberia  https://doi.org/10.21203/rs.3.rs-1993191/v1

Raw data  https://www.ebi.ac.uk/ena/browser/view/PRJNA872874

https://www.mediafire.com/file/gux6blp1g...k.zip/file