GEDmatch Neandertal&Denisov Compare

[SSlava]

You can put your results
This is my result:
Neanderthal (F999902) share for kit
Total SNPs in common: 699460
Match on at least one allele: 553366 (79.1%)
Match on both alleles: 347877 (49.7%)

Denisovian (F999903)
Total SNPs in common: 699220
Match on at least one allele: 555754 (79.5%)
Match on both alleles: 351686 (50.3%)

[SSlava]

It is interesting to compare the results with other

[SSlava]

EUtest Admixture Proportions Neanderthal
SOUTH_BALTIC 0.57%
EAST_EURO 0.89%
NORTH-CENTRAL_EURO 2.49%
ATLANTIC 1.81%
WEST_MED 0.63%
EAST_MED -
WEST_ASIAN -
MIDDLE_EASTERN -
SOUTH_ASIAN -
EAST_AFRICAN -
EAST_ASIAN 2.91%
SIBERIAN 1.50%
WEST_AFRICAN 89.19%

[SSlava]

EUtest Admixture Proportions Denisov
SOUTH_BALTIC -
EAST_EURO 0.99%
NORTH-CENTRAL_EURO 0.52%
ATLANTIC 0.87%
WEST_MED 0.12%
EAST_MED -
WEST_ASIAN -
MIDDLE_EASTERN -
SOUTH_ASIAN -
EAST_AFRICAN -
EAST_ASIAN 1.36%
SIBERIAN 0.72%
WEST_AFRICAN 95.40%

[Insuperable]

EUtest Admixture Proportions Neanderthal
SOUTH_BALTIC 0.57%
EAST_EURO 0.89%
NORTH-CENTRAL_EURO 2.49%
ATLANTIC 1.81%
WEST_MED 0.63%
EAST_MED -
WEST_ASIAN -
MIDDLE_EASTERN -
SOUTH_ASIAN -
EAST_AFRICAN -
EAST_ASIAN 2.91%
SIBERIAN 1.50%
WEST_AFRICAN 89.19%


EUtest Admixture Proportions Denisov
SOUTH_BALTIC -
EAST_EURO 0.99%
NORTH-CENTRAL_EURO 0.52%
ATLANTIC 0.87%
WEST_MED 0.12%
EAST_MED -
WEST_ASIAN -
MIDDLE_EASTERN -
SOUTH_ASIAN -
EAST_AFRICAN -
EAST_ASIAN 1.36%
SIBERIAN 0.72%
WEST_AFRICAN 95.40%

lol

[SSlava]

MDLP World-22 Neanderthal
# Population Percent
1 Sub-Saharian 32.69
2 South-African 31.48
3 Pygmy 27.2
4 East-South-Asian 2.16
5 North-East-European 1.55
6 Atlantic_Mediterranean_Neolithic 1.31
7 Austronesian 1.04
8 East-Siberean 0.65
9 Paleo-Siberian 0.61
10 North-European-Mesolithic 0.46
11 North-Amerind 0.35
12 Samoedic 0.34
13 Indo-Tibetan 0.16

Single Population Sharing:

# Population (source) Distance
1 Biaka_Pygmies (derived) 39.35
2 Ste7 (derived) 52.14
3 Lumbee (derived) 60.83
4 Yemen (derived) 67.1
5 Ethiopian (derived) 67.6
6 Moroccan (derived) 67.65
7 Puerto-Rican (derived) 67.73
8 Jew_Ethiopia (derived) 68.92
9 Uzbek (derived) 69.18
10 Jew-Ethiopia (derived) 69.24
11 Bashkir (derived) 69.72
12 Hazara (derived) 69.78
13 Miwok (derived) 69.81
14 Karakalpak (derived) 69.82
15 Uygur (derived) 70.03
16 Costanoan (derived) 70.09
17 Mozabite (derived) 70.15
18 Australian (derived) 70.2
19 Mexican (derived) 70.35
20 Kazakh (derived) 70.73

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 74.1% Biaka_Pygmies (derived) + 25.9% South-African (ancestral) @ 20.79
2 68.6% Biaka_Pygmies (derived) + 31.4% San (derived) @ 23.03
3 53.2% San (derived) + 46.8% Mbuti_Pygmies (derived) @ 27.88
4 61.6% Biaka_Pygmies (derived) + 38.4% Ste7 (derived) @ 28.35
5 74.5% Biaka_Pygmies (derived) + 25.5% Uzbek (derived) @ 33.41
6 74.7% Biaka_Pygmies (derived) + 25.3% Karakalpak (derived) @ 33.43
7 74.7% Biaka_Pygmies (derived) + 25.3% Bashkir (derived) @ 33.44
8 74.8% Biaka_Pygmies (derived) + 25.2% Uygur (derived) @ 33.45
9 74.7% Biaka_Pygmies (derived) + 25.3% Hazara (derived) @ 33.47
10 75.1% Biaka_Pygmies (derived) + 24.9% Kazakh (derived) @ 33.51
11 75.3% Biaka_Pygmies (derived) + 24.7% Hakas (derived) @ 33.59
12 80.2% Biaka_Pygmies (derived) + 19.8% Bra1 (derived) @ 33.63
13 75.8% Biaka_Pygmies (derived) + 24.2% Tatar_Lithuania (derived) @ 33.63
14 75.4% Biaka_Pygmies (derived) + 24.6% Shor (derived) @ 33.65
15 76.1% Biaka_Pygmies (derived) + 23.9% Colville (derived) @ 33.69
16 75.4% Biaka_Pygmies (derived) + 24.6% Turkmen (derived) @ 33.7
17 76% Biaka_Pygmies (derived) + 24% Kyrgyz (derived) @ 33.74
18 75.9% Biaka_Pygmies (derived) + 24.1% Altaic (derived) @ 33.74
19 75.2% Biaka_Pygmies (derived) + 24.8% Costanoan (derived) @ 33.75
20 76% Biaka_Pygmies (derived) + 24% Nogai (derived) @ 33.81

[Insuperable]

Does this mean that Africans are not Homo sapiens lol or can we apply this techniques on neanderthals at all since reconstructions don't match?

[SSlava]

I do not know what that means))
But denisov is even less "European" autosomes.
Calculator looking like autosomes. But maybe they are very distantly related.

[SSlava]

I think maybe the Africans more "archaic" autosomes.
Or, in fact they are not homo sapiens))

[Insuperable]

I think maybe the Africans more "archaic" autosomes.
Or, in fact they are not homo sapiens))

Reconstructions of Neanderthals look nothing like West Africans. This all is interesting.

[Graham]

Interesting :)

Run it with my fave calculator on Gedmatch
K36 Eurogenes
Denisovan F999902
Pygmy 87.55%
Omotic 2.02%
Oceanian 1.73%
Siberian 1.50%
South_Chinese 1.46%
West_African 1.40%
North_Atlantic 1.23%

Neanderthal F999903

Pygmy 87.17%
West_African 5.86%
Omotic 2.54%
Oceanian 2.28%

[Graham]

SSlava beats me for 'in common SNP's'.

Denisovian (F999903) share for kit M333431:
Total SNPs in common: 686029
Match on at least one allele: 546340 (79.6%)
Match on both alleles: 333304 (48.6%)
------------------------------
Neanderthal (F999902) share for kit M333431:
Total SNPs in common: 686266
Match on at least one allele: 543823 (79.2%)
Match on both alleles: 329466 (48%)

[SSlava]

SSlava beats me for 'in common SNP's'.
I have met with Russian more
Neanderthal (F999902) share for kit
Total SNPs in common: 710551
Match on at least one allele: 561353 (79%)
Match on both alleles: 351497 (49.5%)

[Graham]

Have had a look through MDLPs more European focused runs. Once you take out African links, the closest match is to the Uzbek.

[SSlava]

Interestingly, all these numbers and percentages mean?

[SSlava]

Have had a look through MDLPs more European focused runs. Once you take out African links, the closest match is to the Kazaks.

HM, K5
Population
East_Eurasian 38.41%
West_Eurasian -
Caucasian 30.26%
South_Asian 14.69%
Paleo_mediterranean 16.63%

Population (source) Distance
1 UZ (Uzbek) 21.81
2 NOG (Nogai) 30.22
3 BSHK (Bashkir) 42.27
4 TRK (Turk) 45.79
5 TTR (Tatar) 47.82
6 ASHK (Ashkenazi) 51.62
7 GRK (Greek) 53.83
8 KZK (Kazakh) 54.13
9 SIC (Sicilian) 54.67
10 CHU (Chuvash) 54.94
11 NOSS (North-Ossetian) 55.28
12 GGZ (Gagauz) 55.46
13 RMN (Romanian) 55.58
14 CITAL (Central-Italian) 55.61
15 UD (Udmurt) 55.85
16 MR (Mari) 56.11
17 KSV (Albanian) 56.42
18 CPR (Cypriot) 58.1
19 ADG (Adygei) 58.32
20 BLG (Bulgarian) 58.49

[Graham]

I meant Uzbek lol sorry.:speechless-smiley-0 I ran it yesterday.

[SSlava]

http://verenich.wordpress.com/2013/08/02/%D0%BD%D0%BE%D0%B2%D0%B0%D1%8F-%D1%80%D0%B0%D0%B1%D0%BE%D1%82%D0%B0-%D0%BF%D0%BE-%D0%B3%D0%B5%D0%BD%D0%BE%D0%BC%D1%83-%D0%BD%D0%B5%D0%B0%D0%BD%D0%B4%D0%B5%D1%80%D1%82%D 0%B0%D0%BB%D1%8C%D1%86%D0%B5/

[Thrax]

Neanderthal (M113500) share for kit:
Total SNPs in common: 920177
Match on at least one allele: 732026 (79.6%)
Match on both alleles: 441171 (47.9%)

Denisovian (M071100) share for kit:
Total SNPs in common: 919793
Match on at least one allele: 734998 (79.9%)
Match on both alleles: 445471 (48.4%)

[larali]

What is denisov? (Never mind, I found the info)

Neanderthal:

Total SNPs in common: 921956
Match on at least one allele: 733264 (79.5%)
Match on both alleles: 451962 (49%)

Denisovian:

Total SNPs in common: 921573
Match on at least one allele: 736541 (79.9%)
Match on both alleles: 457171 (49.6%)

[Thrax]

What is denisov?

Google it

[Equilibrium]

Denisovans are a subspecies of Homo-sapiens like Neanderthals, and also extinct. http://en.wikipedia.org/wiki/Denisova_hominin

[Philo]

I have a Gedmatch account. How do I get this done?

[Thrax]

I have a Gedmatch account. How do I get this done?

It's a new option in the "Analyze your data" section

[Equilibrium]

I have a Gedmatch account. How do I get this done?

When you log-in to your gedmatch account you see on the bottom-right corner of the screen the blue blox with the title "Analyze your data". It's the second-last option from that box.

[Equilibrium]

These are my results:

Neanderthal (M113500) share for Equilibrium:
Total SNPs in common: 924069
Match on at least one allele: 730940 (79.1%)
Match on both alleles: 439325 (47.5%)

Denisovian (M071100) share for Equilibrium:
Total SNPs in common: 923704
Match on at least one allele: 734240 (79.5%)
Match on both alleles: 444285 (48.1%)

[Philo]

When you log-in to your gedmatch account you see on the bottom-right corner of the screen the blue blox with the title "Analyze your data". It's the second-last option from that box.


It's a new option in the "Analyze your data" section
Thanks. Here are mine:
Neanderthal:
Neanderthal (M113500) share for Philo:
Total SNPs in common: 902076
Match on at least one allele: 717477 (79.5%)
Match on both alleles: 434400 (48.2%)

Denisovian:
Denisovian (M071100) share for Philo:
Total SNPs in common: 901706
Match on at least one allele: 720064 (79.9%)
Match on both alleles: 438695 (48.7%)

[Mortimer]

Neanderthal ancestry
Total SNPs in common: 932846
Match on at least one allele: 741530 (79.5%)
Match on both alleles: 446037 (47.8%)

Denisovan
Total SNPs in common: 932455
Match on at least one allele: 745268 (79.9%)
Match on both alleles: 451487 (48.4%)

[Oneeye]

Neanderthal (M113500) share for Oneeye:
Total SNPs in common: 920052
Match on at least one allele: 728322 (79.2%)
Match on both alleles: 440668 (47.9%)


Denisovian (M071100) share for Oneeye:
Total SNPs in common: 919669
Match on at least one allele: 731198 (79.5%)
Match on both alleles: 445214 (48.4%)




What's with the Rarest SNP mutations deal?

[Graham]

SSlav you need to run it again, for some reason the results are different.

Neanderthal
Total SNPs in common
932846 -- Gigolo
924069 -- Equilibrium
922406 -- Graham
921956 -- larali
920177 -- paschalisb
920052 -- Oneeye
902076 -- Philo
Match on at least one allele
741530 (79.5%) -- Gigolo
733264 (79.5%) -- larali
732026 (79.6%) -- paschalisb
731909 (79.3%) -- Graham
730940 (79.1%) -- Equilibrium
728322 (79.2%) -- Oneeye
717477 (79.5%) -- Philo
Match on both alleles
451962 (49.0%) -- larali
446037 (47.8%) -- Gigolo
441171 (47.9%) -- paschalisb
440668 (47.9%) -- Oneeye
440350 (47.7%) -- Graham
439325 (47.5%) -- Equilibrium
434400 (48.2%) -- Philo
--------------------------------------------------------
Denisovian
Total SNPs in common
932455 -- Gigolo
923704 -- Equilibrium
922023 -- Graham
921573 -- larali
919793 -- paschalisb
919669 -- Oneeye
901706 -- Philo
Match on at least one allele
745268 (79.9%) -- Gigolo
736541 (79.9%) -- larali
735008 (79.7%) -- Graham
734998 (79.9%) -- paschalisb
734240 (79.5%) -- Equilibrium
731198 (79.5%) -- Oneeye
720064 (79.9%) -- Philo
Match on both alleles
457171 (49.6%) -- larali
451487 (48.4%) -- Gigolo
445471 (48.4%) -- paschalisb
445218 (48.3%) -- Graham
445214 (48.4%) -- Oneeye
444285 (48.1%) -- Equilibrium
438695 (48.7%) -- Philo

[Equilibrium]

Good summary Graham. But note that those who did the comparison early on when the test became available have actually tested against FtDNA versions of Neanderthal and Denisovan samples. They changed the kits later on to 23andme kits, since 23andme tests for more SNPs.

See for example here the difference in total SNPs between your and SSlava's results and the rest (over 200.000 SNPs are missing):

932846 -- Gigolo
924069 -- Equilibrium
921956 -- larali
920177 -- paschalisb
920052 -- Oneeye
902076 -- Philo
699460 -- SSlava
686266 -- Graham

Both of you will have to do the test again, if you want to make a comparison.

[Graham]

I am highly more evolved I'll let you all know. *Snob Mode*

Achh Aye, noticed it, & updated. :P

[MfA_]

BTW It appears to be GEDmatch has optimized further both kits again that total SNPs in common and thus indices have changed drastically.

This was from a week ago:


Neanderthal (M113500) share for MfA
Total SNPs in common: 924069
Match on at least one allele: 715035 (77.4%)
Match on both alleles: 433454 (46.9%)

Denisovian (M071100) share for MfA
Total SNPs in common: 923704
Match on at least one allele: 718106 (77.7%)
Match on both alleles: 438397 (47.5%)


and this is now:


Neanderthal (M113500) share for kit MfA
Total SNPs in common: 899545
Match on at least one allele: 715029 (79.5%)
Match on both alleles: 433448 (48.2%)

Denisovian (M071100) share for kit MfA
Total SNPs in common: 899183
Match on at least one allele: 718098 (79.9%)
Match on both alleles: 438389 (48.8%)

You can see I lost 25k SNPs in common and indices have gone up accordingly..

I think everyone should update their results..

[Equilibrium]

lol I guess there will come more changes in the future.. seems to be a project in development.
Running the comparison analysis felt much longer this time.


Neanderthal (M113500) share for Equilibrium:
Total SNPs in common: 918077
Match on at least one allele: 730938 (79.6%)
Match on both alleles: 439323 (47.9%)


Denisovian (M071100) share for Equilibrium:
Total SNPs in common: 917700
Match on at least one allele: 734239 (80%) New record, I am the most primitive :p
Match on both alleles: 444284 (48.4%)

[Mark]

Neanderthal:
Total SNPs in common: 906006
Match on at least one allele: 720731 (79.6%)
Match on both alleles: 435737 (48.1%)

Denisovian:
Total SNPs in common: 905639
Match on at least one allele: 724026 (79.9%)
Match on both alleles: 440531 (48.6%)

[MfA_]

I shouldn't have used that mouth wash before spitting into the tube, lots of potential have been lost lol..

[Vesuvian Sky]

Neanderthal
Total SNPs in common: 707889
Match on at least one allele: 563369 (79.6%)
Match on both alleles: 350697 (49.5%)

Denisovian
Total SNPs in common: 707639
Match on at least one allele: 566079 (80%)
Match on both alleles: 354832 (50.1%)

[MarkoBravo]

Neanderthal
Total SNPs in common: 682330
Match on at least one allele: 542489 (79.5%)
Match on both alleles: 338757 (49.6%)

Denisovian
Total SNPs in common: 682101
Match on at least one allele: 544565 (79.8%)
Match on both alleles: 342275 (50.2%)

[Stormer99]

I have slightly more in common with both than the average person. Could it be ancient DNA I am unaware of?

Neanderthal
Total SNPs in common: 900579
Match on at least one allele: 721337 (80.1%)
Match on both alleles: 440764 (48.9%)


Denisovian
Total SNPs in common: 900219
Match on at least one allele: 724448 (80.5%)
Match on both alleles: 445522 (49.5%)

[SSlava]

Both of you will have to do the test again, if you want to make a comparison.
All who have 23andMe, far more SNPs?


My result is little changed, fewer SNPs:
Neanderthal (F999902)
Total SNPs in common: 698311
Match on at least one allele: 553366 (79.2%)
Match on both alleles: 347877 (49.8%)

Denisovian (F999903)
Total SNPs in common: 698063
Match on at least one allele: 555752 (79.6%)
Match on both alleles: 351684 (50.4%)

[Equilibrium]

Yes, 23andme tests over 200.000 more SNPs.

[Vesuvian Sky]

Is this tool still on Gedmatch?