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L1983
09-29-2016, 05:31 PM
Forgive my ignorance, but I've just phased my Ancestry kit on gedmatch with my father's and getting very different results to my usual. Are the results literally just telling me the bits I get from my father?! Help!

EG K13 results with paternal phased kit number:
Population
North_Atlantic 55.59
Baltic 21.64
West_Med 18.59
West_Asian 4.18

K13 results with maternal (even though I don't have the dna results yet):
Population
North_Atlantic 38.17
Baltic 20.76
West_Med 11.04
West_Asian 8.32
East_Med 7.02
Red_Sea 1.10
South_Asian 4.49
East_Asian 1.20
Siberian 2.08
Amerindian 1.50
Oceanian -
Northeast_African 0.90
Sub-Saharan 3.43

Edit: Or is phasing used to just distinguish which matches are from which side?

firemonkey
09-29-2016, 06:41 PM
I have heard that Gedmatch phasing is not to be relied on for calculator purposes. I think this is especially true when a phased kit is made for a parent who has not tested their dna. In my case I phased my and my father's kits. The phased kit created for my mother had rather high levels of African; sometimes over 4%. My father's phased and unphased kit ,on the other hand, in many instances was missing anything for African.

L1983
09-29-2016, 06:47 PM
I have heard that Gedmatch phasing is not to be relied on for calculator purposes. I think this is especially true when a phased kit is made for a parent who has not tested their dna. In my case I phased my and my father's kits. The phased kit created for my mother had rather high levels of African; sometimes over 4%. My father's phased and unphased kit ,on the other hand, in many instances was missing anything for African.

Yes I did wonder where my 3+% sub-saharan African came from! I shall wait until my mother's results come through and concentrate on matches for now. :)

firemonkey
09-29-2016, 06:48 PM
My father's phased K13


# Population Percent
1 North_Atlantic 58.99
2 Baltic 24.61
3 West_Med 13.91
4 West_Asian 2.5


My mother's phased K13

1 North_Atlantic 47.40
2 Baltic 21.48
3 West_Med 10.07
4 West_Asian 3.82
5 Northeast_African 3.22
6 East_Asian 2.68
7 Amerindian 2.44
8 Sub-Saharan 2.33
9 South_Asian 2.18
10 East_Med 2.04
11 Red_Sea 1.77

dp
09-29-2016, 08:09 PM
My father's phased K13


# Population Percent
1 North_Atlantic 58.99
2 Baltic 24.61
3 West_Med 13.91
4 West_Asian 2.5


My mother's phased K13

1 North_Atlantic 47.40
2 Baltic 21.48
3 West_Med 10.07
4 West_Asian 3.82
5 Northeast_African 3.22
6 East_Asian 2.68
7 Amerindian 2.44
8 Sub-Saharan 2.33
9 South_Asian 2.18
10 East_Med 2.04
11 Red_Sea 1.77

maternal phase [based on her & my test results]
North_Atlantic 56.68
Baltic 21.58
West_Med 19.27
West_Asian 1.91
East_Med 0.56
[remainder] -

My paternal phase [father not tested, inferred]]
North_Atlantic 46.91
Baltic 21.60
West_Med 18.32
West_Asian 5.24
East_Med 2.08
Red_Sea 2.26
South_Asian 0.43
East_Asian -
Siberian 0.52
Amerindian 1.40
Oceanian -
Northeast_African 0.07
Sub-Saharan 1.16

The results based on my mom & me is a lot less noisy than the phase inferred for my father. Same thing firemonkey encountered with the tests of his father & himself being used to infer his maternal phase.
dp :-)

firemonkey
09-30-2016, 11:08 AM
@DP I notice with your father's inferred results the Northeast African and Sub Saharan is not particularly high.
It seems not all phased kits result in rather high levels of African.

leonardo
09-30-2016, 11:20 AM
@DP I notice with your father's inferred results the Northeast African and Sub Saharan is not particularly high.
It seems not all phased kits result in rather high levels of African.

My phased kit for my father has the same issue. Perhaps it is inherent in the system?

geebee
10-01-2016, 01:00 AM
In my case, only my father has actually tested. My mother, unfortunately, passed away in 2002; otherwise, she'd have loved the idea that she could learn more about her own ancestry through DNA testing.

At any rate, my kit has only been phased using my father's results. For Eurogenes K13, I get these results for his side:


North_Atlantic 52.93
Baltic 21.26
West_Med 15.44
West_Asian 4.80
East_Med 5.57

On my my mother's side I get these results:


North_Atlantic 34.40
Baltic 21.10
West_Med 12.36
West_Asian 8.19
East_Med 6.13
Red_Sea 2.16
South_Asian 3.17
East_Asian 3.15
Siberian 0.99
Amerindian 3.24
Oceanian -
Northeast_African 3.73
Sub-Saharan 1.38

This is [not] entirely unreasonable, because my mother's side actually is more complex than my father's side. As far as we know, he's simply German and British -- all from the colonial era. (I reckon he's probably roughly half-and-half, and that recent ancestry for several generations was likewise about half-and-half.)

In contrast to this, my mother has German, British, Dutch, and Native American ancestry on her father's side; and Spanish (Catalan), German (Alsatian), French, Irish, Swiss, and Native American on her mother's side.

Notice that this list does not include African ancestry, either North African or Sub-Saharan. And very few calculators suggest such ancestry. It isn't impossible, especially considering that my mother's maternal ancestry is from the Deep South; and one of the French ancestors is known to have kept both African and Native American slaves.

The mother of his son and daughter (or the mothers of each of them, if they did not have the same mother) may have been included among the latter. He did eventually marry the mother of his son -- who may or may not have been the same as the mother of his daughter. (If they were two different women, both were Native American.)

Even so, very few calculators have found any significant amount of African ancestry. It's possible, but I would doubt the 3.73% Northeast African or the 1.38% Sub-Saharan.

And while I definitely do have the Native American, the number seems at least somewhat inflated at 3.73%. At Ancestry, it's only 1%; and 2% at 23andMe.

For comparison, here are the results for my unphased kit:


North_Atlantic 42.70
Baltic 21.50
West_Med 13.78
West_Asian 7.47
East_Med 7.66
Red_Sea 1.47
South_Asian 0.84
East_Asian 1.47
Siberian 0.36
Amerindian 2.19
Oceanian -
Northeast_African 0.56

Notice that the "Amerindian" component here is more in line with 23andMe's estimate. However, there's also 1.47% "East Asian" here, which 23andMe does not indicate. Also, while there is no Sub-Saharan African here, there is 0.56% Northeast African -- neither of which is suggested either by 23andMe or Ancestry.

L1983
10-01-2016, 01:00 PM
In my case, only my father has actually tested. My mother, unfortunately, passed away in 2002; otherwise, she'd have loved the idea that she could learn more about her own ancestry through DNA testing.

At any rate, my kit has only been phased using my father's results. For Eurogenes K13, I get these results for his side:


North_Atlantic 52.93
Baltic 21.26
West_Med 15.44
West_Asian 4.80
East_Med 5.57

On my my mother's side I get these results:


North_Atlantic 34.40
Baltic 21.10
West_Med 12.36
West_Asian 8.19
East_Med 6.13
Red_Sea 2.16
South_Asian 3.17
East_Asian 3.15
Siberian 0.99
Amerindian 3.24
Oceanian -
Northeast_African 3.73
Sub-Saharan 1.38

This is [not] entirely unreasonable, because my mother's side actually is more complex than my father's side. As far as we know, he's simply German and British -- all from the colonial era. (I reckon he's probably roughly half-and-half, and that recent ancestry for several generations was likewise about half-and-half.)

In contrast to this, my mother has German, British, Dutch, and Native American ancestry on her father's side; and Spanish (Catalan), German (Alsatian), French, Irish, Swiss, and Native American on her mother's side.

Notice that this list does not include African ancestry, either North African or Sub-Saharan. And very few calculators suggest such ancestry. It isn't impossible, especially considering that my mother's maternal ancestry is from the Deep South; and one of the French ancestors is known to have kept both African and Native American slaves.

The mother of his son and daughter (or the mothers of each of them, if they did not have the same mother) may have been included among the latter. He did eventually marry the mother of his son -- who may or may not have been the same as the mother of his daughter. (If they were two different women, both were Native American.)

Even so, very few calculators have found any significant amount of African ancestry. It's possible, but I would doubt the 3.73% Northeast African or the 1.38% Sub-Saharan.

And while I definitely do have the Native American, the number seems at least somewhat inflated at 3.73%. At Ancestry, it's only 1%; and 2% at 23andMe.

For comparison, here are the results for my unphased kit:


North_Atlantic 42.70
Baltic 21.50
West_Med 13.78
West_Asian 7.47
East_Med 7.66
Red_Sea 1.47
South_Asian 0.84
East_Asian 1.47
Siberian 0.36
Amerindian 2.19
Oceanian -
Northeast_African 0.56

Notice that the "Amerindian" component here is more in line with 23andMe's estimate. However, there's also 1.47% "East Asian" here, which 23andMe does not indicate. Also, while there is no Sub-Saharan African here, there is 0.56% Northeast African -- neither of which is suggested either by 23andMe or Ancestry.

Thank you for the analysis.

On a side note, I was wondering if you'd mind sharing your gedmatch with me at all? My dad gets 1% Native American on Ancestry and I'm trying to figure out if it's real or not and whether he gets similar levels to yours. Feel free to PM me :)