List of biased SNPs for qpadm

[Genetics189291]

For example, in the G25 sheet you have Turkey_N.DG, Turkey_N.SG, Turkey_N_noUDG, Turkey_N, and you can use all four interchangeably, all can act well as an EEF source.
In qpadm the model can fail if you replace  Turkey_N.DG with  Turkey_N.

Doesn’t that make g25 inaccurate in that instance then?

No, it makes G25 more reliable because it can recognize these are all the same population and isn't distracted by chip differences.

Yeah they’re the same populations with genetic differences for example on global25 Turkey.DG has more Levantine ancestry and .SG gives completely different results, both differ from the normal Turkey_N samples so you have a decent amount of genetic variation in these samples

[nomad01]

Doesn’t that make g25 inaccurate in that instance then?

No, it makes G25 more reliable because it can recognize these are all the same population and isn't distracted by chip differences.

Yeah they’re the same populations with genetic differences for example on global25 Turkey.DG has more Levantine ancestry and .SG gives completely different results, both differ from the normal Turkey_N samples so you have a decent amount of genetic variation in these samples

What about these? All 3 are the same sample

Code:

TUR_Marmara_Barcin_N:I1583,0.119514,0.180764,0.00264,-0.10756,0.048932,-0.051037,-0.010575,-0.008769,0.035792,0.087656,0.012342,0.012139,-0.023786,0.005092,-0.036644,-0.006497,0.020861,0.002534,0.011816,-0.003877,-0.011729,0.004822,0.001232,-0.006748,-0.00491
Turkey_N:I1583_enhanced,0.1161,0.185842,0.005657,-0.107883,0.050163,-0.046017,-0.00564,-0.006,0.039882,0.084193,0.015752,0.009741,-0.022596,0.002202,-0.037323,-0.008088,0.018645,0.00228,0.009804,-0.004377,-0.012228,0.006183,-0.002465,-0.009158,-0.003712
Turkey_N.DG:I1583.DG,0.117238,0.183811,0.000754,-0.107237,0.052933,-0.052431,-0.00282,-0.011538,0.045404,0.08638,0.010393,0.004646,-0.017393,0.002477,-0.040716,-0.006762,0.02034,0.003167,0.013324,0.000625,-0.009234,0.009645,-0.00037,-0.010363,-0.011256

[Genetics189291]

No, it makes G25 more reliable because it can recognize these are all the same population and isn't distracted by chip differences.

Yeah they’re the same populations with genetic differences for example on global25 Turkey.DG has more Levantine ancestry and .SG gives completely different results, both differ from the normal Turkey_N samples so you have a decent amount of genetic variation in these samples

What about these? All 3 are the same sample

Code:

TUR_Marmara_Barcin_N:I1583,0.119514,0.180764,0.00264,-0.10756,0.048932,-0.051037,-0.010575,-0.008769,0.035792,0.087656,0.012342,0.012139,-0.023786,0.005092,-0.036644,-0.006497,0.020861,0.002534,0.011816,-0.003877,-0.011729,0.004822,0.001232,-0.006748,-0.00491
Turkey_N:I1583_enhanced,0.1161,0.185842,0.005657,-0.107883,0.050163,-0.046017,-0.00564,-0.006,0.039882,0.084193,0.015752,0.009741,-0.022596,0.002202,-0.037323,-0.008088,0.018645,0.00228,0.009804,-0.004377,-0.012228,0.006183,-0.002465,-0.009158,-0.003712
Turkey_N.DG:I1583.DG,0.117238,0.183811,0.000754,-0.107237,0.052933,-0.052431,-0.00282,-0.011538,0.045404,0.08638,0.010393,0.004646,-0.017393,0.002477,-0.040716,-0.006762,0.02034,0.003167,0.013324,0.000625,-0.009234,0.009645,-0.00037,-0.010363,-0.011256

Target: Son_scaled
Distance: 1.5201% / 0.01520094
39.4 Turkey_N.DG
25.0 IBM
14.6 SSA
11.2 Steppe
4.2 Levant_Meoslithic
2.2 Nilo-Saharian_Pastoralist
2.0 Iran_N
1.4 AUS_Willandra_Lakes_4000BP

Target: Son_scaled
Distance: 1.1688% / 0.01168779
38.6 Turkey_N
24.0 IBM
14.8 SSA
10.2 Steppe
6.6 Levant_Meoslithic
2.0 AUS_Willandra_Lakes_4000BP
2.0 Nilo-Saharian_Pastoralist
1.8 Iran_N

Target: Son_scaled
Distance: 1.2719% / 0.01271855
37.8 TUR_Marmara_Barcin_N
24.0 IBM
14.6 SSA
10.8 Steppe
6.8 Levant_Meoslithic
2.6 Nilo-Saharian_Pastoralist
1.6 Iran_N
1.4 AUS_Willandra_Lakes_4000BP
0.4 WHG

Turkey.DG having the biggest difference the first two are quiet similar since one is just enhanced

[Genetics189291]

No, it makes G25 more reliable because it can recognize these are all the same population and isn't distracted by chip differences.

Yeah they’re the same populations with genetic differences for example on global25 Turkey.DG has more Levantine ancestry and .SG gives completely different results, both differ from the normal Turkey_N samples so you have a decent amount of genetic variation in these samples

What about these? All 3 are the same sample

Code:

TUR_Marmara_Barcin_N:I1583,0.119514,0.180764,0.00264,-0.10756,0.048932,-0.051037,-0.010575,-0.008769,0.035792,0.087656,0.012342,0.012139,-0.023786,0.005092,-0.036644,-0.006497,0.020861,0.002534,0.011816,-0.003877,-0.011729,0.004822,0.001232,-0.006748,-0.00491
Turkey_N:I1583_enhanced,0.1161,0.185842,0.005657,-0.107883,0.050163,-0.046017,-0.00564,-0.006,0.039882,0.084193,0.015752,0.009741,-0.022596,0.002202,-0.037323,-0.008088,0.018645,0.00228,0.009804,-0.004377,-0.012228,0.006183,-0.002465,-0.009158,-0.003712
Turkey_N.DG:I1583.DG,0.117238,0.183811,0.000754,-0.107237,0.052933,-0.052431,-0.00282,-0.011538,0.045404,0.08638,0.010393,0.004646,-0.017393,0.002477,-0.040716,-0.006762,0.02034,0.003167,0.013324,0.000625,-0.009234,0.009645,-0.00037,-0.010363,-0.011256

From what I know turkey_n.dg has the highest coverage 99. Percent I think it was around 99.86 or something around that so it’s the highest coverage turkey_n sample we have