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Kurd
05-03-2016, 05:02 AM
I will be posting some IBS comparisons with various recently sequenced genomes that were referenced in a recent paper "The genetic history of Ice Age Europe" by Fu et al. The number of SNPs used is limited to overlapping SNPs with V4 genotyped project members.

IBS comparisons entail total drift / accumulated mutation comparisons, and are thus in a sense different from dstats, and allele frequency admixture calculator outputs which group samples based on recent drift.



NO
SAMPLE
IBS EL MIRON (81K SNPs) - SPAIN-18kya


1
ElMiron
100.00%


2
Bichon
73.10%


3
LaBrana1
69.55%


4
Loschbour
69.52%


5
Kotias
69.37%


6
Ranchot88
69.30%


7
Rochedane
69.24%


8
GoyetQ116-1
68.69%


9
Villabruna
68.65%


10
Ostuni1
67.89%


11
Hungarian.KO1
67.81%


12
KremsWA3
67.73%


13
Vestonice16
67.45%


14
Motala12
67.27%


15
Kostenki14
66.65%


16
Andronovo2
66.09%


17
Andronovo1
66.09%


18
Potapovka
66.09%


19
Samara_HG
66.00%


20
Lithuanian
65.99%


21
Karelia
65.97%


22
Samara_Eneolithic
65.96%


23
AfontovaGora3
65.87%


24
Poltavka_outlier
65.87%


25
Kumtepe006
65.84%


26
Karasuk7
65.74%


27
.Krefter
65.72%


28
Srubnaya
65.70%


29
Srubnaya_Outlier
65.69%


30
Andronovo3
65.69%


31
.Passa
65.63%


32
Malta1
65.61%


33
Andronovo4
65.58%


34
Poltavka
65.57%


35
.Powell
65.56%


36
Karasuk5
65.54%


37
Anatolia_Neolithic
65.45%


38
Karasuk8
65.41%


39
Scythian_IA
65.39%


40
Stuttgart
65.31%


41
Karasuk4
65.30%


42
.McNinjaMom
65.23%


43
.Mfa
65.22%


44
.Znertu
65.22%


45
Starcevo_EN
65.22%


46
.Hanna_GF
65.19%


47
.Dluffy
65.15%


48
Karasuk2
65.14%


49
.NK19191
65.14%


50
.Kurd_Ezidi
65.14%


51
.Zephyrous
65.13%


52
.Hanna_A
65.09%


53
Paniyas
65.07%


54
.Balq
65.05%


55
.Sapporo
65.03%


56
.Halgurd
65.00%


57
.Kurd_C4
65.00%


58
.Rukha
65.00%


59
.Punjabi_Rajput
64.99%


60
Onge
64.97%


61
.Hanna
64.97%


62
.Bored
64.97%


63
.Jatt_Har393
64.97%


64
.Gill
64.96%


65
Palliyar
64.95%


66
.McNinja
64.95%


67
.Khana
64.94%


68
Oase1
64.93%


69
.Parasar
64.92%


70
.Melif
64.91%


71
.Kaido
64.89%


72
.Kurd_C3
64.88%


73
UstIshim
64.88%


74
BedouinB
64.87%


75
.Kurd_SE
64.87%


76
.Jam
64.87%


77
.Pak_Gujjar
64.86%


78
.Hanif
64.86%


79
.Kurd_C2
64.85%


80
.Sein
64.85%


81
.Kenji
64.85%


82
.Varun
64.84%


83
.Sadia
64.82%


84
.Arbogan
64.82%


85
.Farid
64.82%


86
.Bol_Nat
64.81%


87
.Arain_Sheikh
64.81%


88
.Pahari
64.81%


89
.Reza1
64.80%


90
Karasuk6
64.78%


91
.DMXX
64.76%


92
.Zara
64.74%


93
Satsurblia
64.73%


94
.Kandhari
64.68%


95
.Kurd_C1
64.66%


96
Karitiana
64.61%


97
.Ashwin
64.58%


98
Nganasan
64.58%


99
.Jesus
64.45%


100
Papuan
64.33%


101
Dai
64.27%


102
.Awale
63.35%


103
.MOTA
62.40%


104
MbutiPygmy
62.01%


105
Yoruba
61.90%


106
Denisovan
61.80%

Kurd
05-03-2016, 05:09 AM
NO
SAMPLE
IBS AFONTOVA GORA 3 (35K SNPs) - RUSSIA - 16 kya


1
AfontovaGora3
100.00%


2
Kotias
69.80%


3
Malta1
69.37%


4
Samara_HG
68.88%


5
Karelia
68.86%


6
Bichon
68.70%


7
Samara_Eneolithic
68.32%


8
Andronovo4
67.91%


9
Srubnaya_Outlier
67.45%


10
Motala12
67.22%


11
Karitiana
67.05%


12
Poltavka
66.71%


13
Andronovo3
66.71%


14
Andronovo2
66.70%


15
Karasuk7
66.65%


16
Karasuk5
66.59%


17
Karasuk8
66.58%


18
Scythian_IA
66.57%


19
Karasuk2
66.56%


20
Karasuk4
66.48%


21
Potapovka
66.25%


22
Srubnaya
66.24%


23
Karasuk6
66.00%


24
Andronovo1
65.94%


25
ElMiron
65.87%


26
LaBrana1
65.85%


27
Poltavka_outlier
65.82%


28
Lithuanian
65.77%


29
Paniyas
65.73%


30
Vestonice16
65.70%


31
KremsWA3
65.69%


32
.Bol_Nat
65.67%


33
.Bored
65.67%


34
GoyetQ116-1
65.67%


35
.Balq
65.66%


36
.Kenji
65.64%


37
Palliyar
65.61%


38
.Melif
65.61%


39
.Rukha
65.60%


40
.Hanif
65.59%


41
Villabruna
65.55%


42
.Sein
65.54%


43
.Sapporo
65.53%


44
Nganasan
65.53%


45
Hungarian.KO1
65.53%


46
.Punjabi_Rajput
65.53%


47
.Parasar
65.51%


48
.Gill
65.49%


49
Kostenki14
65.48%


50
Satsurblia
65.46%


51
.Jam
65.45%


52
Rochedane
65.43%


53
Oase1
65.42%


54
.Khana
65.41%


55
.Kaido
65.40%


56
.McNinja
65.39%


57
.Dluffy
65.39%


58
Loschbour
65.38%


59
.Jatt_Har393
65.38%


60
.Pak_Gujjar
65.37%


61
.McNinjaMom
65.37%


62
.Mfa
65.37%


63
.Krefter
65.37%


64
.Zara
65.34%


65
.NK19191
65.32%


66
Kumtepe006
65.30%


67
.Znertu
65.29%


68
.Arain_Sheikh
65.29%


69
.Pahari
65.29%


70
.Ashwin
65.26%


71
.Powell
65.23%


72
Ranchot88
65.16%


73
Onge
65.15%


74
.Kurd_SE
65.15%


75
Ostuni1
65.14%


76
.Sadia
65.09%


77
.Varun
65.09%


78
.Kandhari
65.08%


79
.DMXX
65.04%


80
.Halgurd
65.02%


81
.Kurd_C4
65.02%


82
.Reza1
64.98%


83
.Arbogan
64.96%


84
Starcevo_EN
64.94%


85
.Kurd_C2
64.93%


86
.Kurd_Ezidi
64.93%


87
.Passa
64.92%


88
.Hanna_A
64.85%


89
.Hanna_GF
64.84%


90
.Zephyrous
64.81%


91
.Hanna
64.81%


92
.Farid
64.80%


93
.Kurd_C3
64.78%


94
Papuan
64.75%


95
Anatolia_Neolithic
64.64%


96
.Jesus
64.60%


97
.Kurd_C1
64.59%


98
UstIshim
64.47%


99
Dai
64.45%


100
Stuttgart
64.40%


101
BedouinB
64.35%


102
.Awale
62.99%


103
.MOTA
62.37%


104
Denisovan
61.71%


105
Yoruba
61.59%


106
MbutiPygmy
61.52%

Kurd
05-03-2016, 05:21 AM
To be continued tomorrow



NO
SAMPLE
IBS GOYET Q116 (80K SNPs) - BELGIUM-35kya


1
GoyetQ116-1
100.00%


2
Bichon
69.25%


3
Kotias
68.92%


4
ElMiron
68.69%


5
Ostuni1
67.14%


6
LaBrana1
67.06%


7
KremsWA3
67.00%


8
Vestonice16
66.86%


9
Kostenki14
66.77%


10
Rochedane
66.64%


11
Loschbour
66.59%


12
Ranchot88
66.26%


13
Villabruna
66.06%


14
Andronovo4
65.81%


15
Hungarian.KO1
65.78%


16
AfontovaGora3
65.67%


17
Kumtepe006
65.65%


18
Samara_HG
65.63%


19
Motala12
65.63%


20
Malta1
65.58%


21
Karelia
65.36%


22
Andronovo1
65.29%


23
Samara_Eneolithic
65.29%


24
Poltavka_outlier
65.27%


25
Karasuk5
65.27%


26
Potapovka
65.26%


27
Andronovo3
65.23%


28
UstIshim
65.18%


29
Srubnaya_Outlier
65.08%


30
Onge
65.04%


31
Lithuanian
65.02%


32
Srubnaya
65.02%


33
.Krefter
64.99%


34
Andronovo2
64.97%


35
Oase1
64.96%


36
Stuttgart
64.94%


37
.Bol_Nat
64.93%


38
Karasuk7
64.92%


39
Paniyas
64.90%


40
Scythian_IA
64.89%


41
.Balq
64.87%


42
.Powell
64.85%


43
Anatolia_Neolithic
64.84%


44
Karasuk2
64.84%


45
Poltavka
64.81%


46
Karasuk4
64.78%


47
Palliyar
64.76%


48
.Znertu
64.75%


49
.Hanif
64.74%


50
Karasuk6
64.71%


51
.Varun
64.69%


52
Karasuk8
64.69%


53
.Kenji
64.69%


54
.Sein
64.68%


55
.Jam
64.68%


56
.Khana
64.68%


57
.Halgurd
64.67%


58
.Kurd_C4
64.67%


59
.Kurd_Ezidi
64.66%


60
.Bored
64.66%


61
Satsurblia
64.65%


62
.Kandhari
64.64%


63
.Sadia
64.64%


64
.Melif
64.63%


65
.Punjabi_Rajput
64.63%


66
.McNinjaMom
64.63%


67
.Jatt_Har393
64.61%


68
.Dluffy
64.60%


69
.Gill
64.58%


70
.Reza1
64.54%


71
.NK19191
64.54%


72
.Ashwin
64.53%


73
.Hanna
64.53%


74
.Rukha
64.53%


75
.Arain_Sheikh
64.53%


76
.Pahari
64.53%


77
.Kaido
64.53%


78
.Arbogan
64.52%


79
.Parasar
64.52%


80
.Passa
64.51%


81
.Kurd_C2
64.50%


82
.Kurd_C3
64.50%


83
.Farid
64.49%


84
.Pak_Gujjar
64.49%


85
.Zephyrous
64.48%


86
.Sapporo
64.47%


87
Papuan
64.47%


88
BedouinB
64.45%


89
Karitiana
64.45%


90
.DMXX
64.44%


91
.Kurd_SE
64.43%


92
.McNinja
64.42%


93
.Mfa
64.40%


94
.Hanna_A
64.40%


95
.Kurd_C1
64.38%


96
Starcevo_EN
64.37%


97
.Hanna_GF
64.37%


98
.Jesus
64.37%


99
Nganasan
64.34%


100
.Zara
64.33%


101
Dai
64.28%


102
.Awale
63.33%


103
.MOTA
62.42%


104
MbutiPygmy
61.91%


105
Yoruba
61.90%


106
Denisovan
61.80%

Padre Organtino
05-03-2016, 07:39 AM
What's up with very large IBS scores for Kotias?

Kurd
05-03-2016, 01:47 PM
My guess is that Kumtepe would be at the top of the table, had it not been for it having about 50K SNPs no call SNPs, for which Satsurbila had calls. To put Kumtepe on a level playing field, I would have to prune about 50K SNPs from most samples.




NO
SAMPLE
IBS SATSURBILA (80K SNPs) - GEORGIA- 13 kya


1
Satsurblia
100.00%


2
Kotias
74.41%


3
Bichon
67.81%


4
Kumtepe006
66.74%


5
Andronovo1
66.16%


6
.Znertu
66.14%


7
.Hanna_A
66.05%


8
.Hanna_GF
66.01%


9
Poltavka
65.99%


10
.Kurd_Ezidi
65.99%


11
.Hanna
65.96%


12
.Kurd_C3
65.88%


13
.Jesus
65.87%


14
.Arbogan
65.86%


15
Poltavka_outlier
65.85%


16
.NK19191
65.85%


17
.Kurd_C2
65.84%


18
.Kurd_C1
65.82%


19
.Zephyrous
65.81%


20
.Mfa
65.80%


21
.Halgurd
65.78%


22
.Kurd_C4
65.78%


23
.DMXX
65.78%


24
.Farid
65.75%


25
.Bol_Nat
65.74%


26
Potapovka
65.73%


27
.Kurd_SE
65.72%


28
.Sapporo
65.72%


29
.Rukha
65.71%


30
.Kandhari
65.71%


31
Andronovo2
65.66%


32
Srubnaya
65.66%


33
Srubnaya_Outlier
65.65%


34
.Pak_Gujjar
65.64%


35
.Punjabi_Rajput
65.63%


36
.Sein
65.63%


37
.Arain_Sheikh
65.63%


38
.Pahari
65.63%


39
.Melif
65.63%


40
.Zara
65.61%


41
.Khana
65.59%


42
Lithuanian
65.58%


43
.Powell
65.57%


44
Samara_Eneolithic
65.57%


45
.Kaido
65.55%


46
.Hanif
65.54%


47
Scythian_IA
65.54%


48
.Jatt_Har393
65.54%


49
.Kenji
65.51%


50
.Passa
65.50%


51
.McNinjaMom
65.49%


52
.Jam
65.48%


53
.Krefter
65.46%


54
.McNinja
65.46%


55
Starcevo_EN
65.46%


56
AfontovaGora3
65.46%


57
.Ashwin
65.46%


58
.Dluffy
65.43%


59
Andronovo3
65.41%


60
Stuttgart
65.40%


61
Karasuk7
65.39%


62
.Gill
65.38%


63
.Bored
65.35%


64
Karasuk5
65.31%


65
Karasuk8
65.30%


66
BedouinB
65.30%


67
.Sadia
65.25%


68
.Balq
65.24%


69
Anatolia_Neolithic
65.22%


70
.Varun
65.22%


71
Karelia
65.21%


72
.Parasar
65.20%


73
Samara_HG
65.19%


74
Motala12
65.11%


75
Loschbour
65.08%


76
Andronovo4
65.06%


77
Karasuk4
65.03%


78
.Reza1
64.97%


79
Karasuk2
64.94%


80
Kostenki14
64.90%


81
Paniyas
64.89%


82
Hungarian.KO1
64.87%


83
LaBrana1
64.84%


84
Palliyar
64.84%


85
Vestonice16
64.77%


86
Malta1
64.74%


87
KremsWA3
64.73%


88
ElMiron
64.73%


89
Villabruna
64.70%


90
GoyetQ116-1
64.65%


91
Ostuni1
64.65%


92
Karasuk6
64.50%


93
Onge
64.39%


94
Karitiana
64.38%


95
Rochedane
64.30%


96
Papuan
64.14%


97
UstIshim
64.10%


98
Nganasan
64.08%


99
Ranchot88
64.07%


100
Dai
64.04%


101
.Awale
63.30%


102
Oase1
63.30%


103
.MOTA
62.68%


104
Yoruba
62.08%


105
MbutiPygmy
62.01%


106
Denisovan
61.66%

Halgurd
05-04-2016, 09:10 PM
56 .Halgurd 65.00%
57 .Kurd_C4 65.00%

80 .Halgurd 65.02%
81 .Kurd_C4 65.02%

57 .Halgurd 64.67%
58 .Kurd_C4 64.67%

21 .Halgurd 65.78%
22 .Kurd_C4 65.78%

We score the exact same for everything.