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Population genetics studies: Genetic Lineages of North Lebanon
#16
Extracted the SNPs using v54p1_1240K_clean.snplist

719665 variants loaded from .bim file
295 people (90 males, 198 females, 7 ambiguous)
--extract 411826 variants remaining
Total genotyping rate is 0.979425

NET: About a third of the SNPs from 1240K are represented in the data.

Below is the coverage within those 411K SNPs
Code:
IID                    F_MISS            Coverage
9238348109_R04C01    0.000496    0.999504
9236445147_R03C02    0.0005033    0.9994967
9236445147_R02C02    0.0005058    0.9994942
9236445147_R05C02    0.0005269    0.9994731
9236445226_R05C01    0.0005374    0.9994626
9236445147_R06C01    0.000552    0.999448
9236445226_R04C01    0.000569    0.999431
9236445147_R01C02    0.0005714    0.9994286
9236445147_R06C02    0.0005738    0.9994262
9236445147_R05C01    0.0005933    0.9994067
9238348033_R06C01    0.0005973    0.9994027
9236445226_R03C01    0.0006079    0.9993921
9236445147_R04C02    0.0006152    0.9993848
9236445178_R05C02    0.0006176    0.9993824
9236445226_R05C02    0.0006176    0.9993824
9236445231_R02C02    0.0006176    0.9993824
9236445226_R01C02    0.00062    0.99938
9238348033_R02C01    0.0006216    0.9993784
9236445231_R04C01    0.0006289    0.9993711
9236445226_R03C02    0.0006459    0.9993541
9238348033_R06C02    0.0006735    0.9993265
9236445178_R04C01    0.0006784    0.9993216
9236445226_R04C02    0.0006857    0.9993143
9236445231_R05C01    0.0007149    0.9992851
9238349138_R06C01    0.0007173    0.9992827
9236445178_R05C01    0.0007343    0.9992657
9236445226_R02C02    0.0007357    0.9992643
9236445231_R03C01    0.0007392    0.9992608
9238348051_R05C02    0.0007465    0.9992535
9238348109_R02C01    0.0007562    0.9992438
9236445231_R06C01    0.0007732    0.9992268
9238349138_R05C01    0.0007781    0.9992219
9236445147_R04C01    0.0007795    0.9992205
9236445231_R04C02    0.0007903    0.9992097
9238348109_R02C02    0.0007989    0.9992011
9238348033_R03C01    0.0008037    0.9991963
9236445231_R03C02    0.0008146    0.9991854
9238348109_R06C01    0.0008194    0.9991806
9236445178_R02C02    0.0008243    0.9991757
9238348109_R05C02    0.0008316    0.9991684
9238348017_R06C02    0.0008413    0.9991587
9236445231_R06C02    0.0008632    0.9991368
9236445226_R06C01    0.0008669    0.9991331
9236445178_R03C01    0.0008814    0.9991186
9236445231_R01C02    0.0008814    0.9991186
9238348109_R06C02    0.0008851    0.9991149
9238348033_R04C01    0.0008972    0.9991028
9238349138_R06C02    0.0009251    0.9990749
9236445226_R01C01    0.0009386    0.9990614
9236445178_R04C02    0.000947    0.999053
9236445178_R06C02    0.000964    0.999036
9236445226_R02C01    0.0009689    0.9990311
9236445231_R05C02    0.0009775    0.9990225
9238348051_R06C02    0.0009823    0.9990177
9236445178_R03C02    0.0009896    0.9990104
9238348109_R04C02    0.001003    0.998997
9236445178_R06C01    0.001015    0.998985
9236445178_R01C02    0.001025    0.998975
9236445178_R02C01    0.001026    0.998974
9238349138_R02C01    0.001031    0.998969
9238348049_R02C02    0.001046    0.998954
9238348095_R06C02    0.001049    0.998951
9236445231_R01C01    0.001055    0.998945
9238348109_R01C02    0.00106    0.99894
9238388031_R02C02    0.001063    0.998937
9238388031_R02C01    0.001075    0.998925
9236445231_R02C01    0.001081    0.998919
9238348152_R06C01    0.001082    0.998918
9238348033_R05C02    0.001089    0.998911
9236445178_R01C01    0.001099    0.998901
9238349138_R05C02    0.0011    0.9989
9238348152_R05C01    0.001119    0.998881
9238348033_R02C02    0.001172    0.998828
9238348049_R05C01    0.001177    0.998823
9236445226_R06C02    0.0012    0.9988
9238348095_R06C01    0.001218    0.998782
9238348055_R06C01    0.001221    0.998779
9238348152_R03C01    0.001277    0.998723
9238348055_R02C02    0.001281    0.998719
9238348152_R06C02    0.001298    0.998702
9238348152_R02C02    0.001335    0.998665
9238348152_R04C02    0.001337    0.998663
9238348033_R05C01    0.001345    0.998655
9238348049_R02C01    0.00135    0.99865
9238348049_R03C01    0.001357    0.998643
9238349138_R03C01    0.001374    0.998626
9238348083_R02C02    0.001384    0.998616
9238348033_R03C02    0.001405    0.998595
9238348033_R01C01    0.00141    0.99859
9238348152_R04C01    0.001445    0.998555
9238388031_R04C01    0.001452    0.998548
9238348152_R03C02    0.001454    0.998546
9238388031_R01C01    0.001466    0.998534
9238388031_R06C01    0.001469    0.998531
9238348049_R05C02    0.001483    0.998517
9238348049_R01C01    0.001518    0.998482
9238348083_R05C02    0.001527    0.998473
9238388031_R03C01    0.001527    0.998473
9238348095_R02C02    0.001542    0.998458
9238348055_R02C01    0.001546    0.998454
9238348152_R01C01    0.001551    0.998449
9238348109_R01C01    0.001554    0.998446
9238348055_R05C02    0.001602    0.998398
9238348055_R04C01    0.001615    0.998385
9238348152_R02C01    0.001622    0.998378
9238348083_R03C02    0.001649    0.998351
9238348152_R05C02    0.001658    0.998342
9238348049_R03C02    0.001692    0.998308
9238348049_R06C01    0.001712    0.998288
9238388031_R05C01    0.001734    0.998266
9236442156_R01C02    0.001748    0.998252
9238388031_R01C02    0.001775    0.998225
9238348083_R01C02    0.001787    0.998213
9236442156_R01C01    0.00179    0.99821
9238348049_R01C02    0.001799    0.998201
9238348152_R01C02    0.001819    0.998181
9238348051_R03C02    0.001821    0.998179
9238349138_R01C02    0.001833    0.998167
9238348055_R01C01    0.001843    0.998157
9238348055_R04C02    0.00185    0.99815
9238348033_R01C02    0.001853    0.998147
9238348055_R03C01    0.001858    0.998142
9238348055_R06C02    0.00186    0.99814
9238348083_R01C01    0.00186    0.99814
9238348049_R06C02    0.001892    0.998108
9238348083_R04C02    0.001894    0.998106
9238348049_R04C01    0.001904    0.998096
9238349138_R01C01    0.001931    0.998069
9238349138_R04C02    0.001982    0.998018
9238348095_R01C02    0.002028    0.997972
9238348083_R04C01    0.002042    0.997958
9238349138_R02C02    0.002047    0.997953
9238348055_R05C01    0.002049    0.997951
9236442156_R02C02    0.002081    0.997919
9238348095_R02C01    0.002125    0.997875
9238348095_R04C01    0.002193    0.997807
9238348055_R01C02    0.002202    0.997798
9238348049_R04C02    0.002212    0.997788
9238388031_R05C02    0.002215    0.997785
9238348083_R02C01    0.002244    0.997756
9238348033_R04C02    0.002266    0.997734
9238349138_R03C02    0.002283    0.997717
9238348095_R05C01    0.002327    0.997673
9236442156_R06C02    0.002395    0.997605
9236442156_R03C02    0.002467    0.997533
9238348095_R04C02    0.002486    0.997514
9238388031_R03C02    0.0025    0.9975
9238348083_R06C02    0.002512    0.997488
9238349138_R04C01    0.002517    0.997483
9236445201_R05C01    0.002552    0.997448
9236442156_R03C01    0.002587    0.997413
9236445201_R05C02    0.002604    0.997396
9236442156_R02C01    0.002682    0.997318
9236442156_R06C01    0.002715    0.997285
9238348095_R01C01    0.002787    0.997213
9238348012_R05C01    0.002862    0.997138
9238388031_R04C02    0.002897    0.997103
9238348095_R03C01    0.002907    0.997093
9236442156_R04C02    0.003049    0.996951
9236445201_R06C01    0.003066    0.996934
9236442156_R04C01    0.003258    0.996742
9236442156_R05C02    0.003436    0.996564
9238348083_R06C01    0.003528    0.996472
9238348055_R03C02    0.003647    0.996353
9236445201_R03C01    0.003881    0.996119
9236445201_R04C02    0.003997    0.996003
9238348135_R04C02    0.004141    0.995859
9238348095_R03C02    0.004224    0.995776
9236445206_R06C02    0.00426    0.99574
9236445201_R06C02    0.004262    0.995738
9236442156_R05C01    0.004393    0.995607
9236445201_R03C02    0.005019    0.994981
9238348012_R06C01    0.005101    0.994899
9238348109_R03C02    0.005109    0.994891
9238348135_R05C02    0.005201    0.994799
9238388031_R06C02    0.005364    0.994636
9236445206_R05C02    0.005473    0.994527
9238348095_R05C02    0.005593    0.994407
9236445201_R02C01    0.005687    0.994313
9238348135_R06C02    0.005922    0.994078
9236442092_R06C01    0.007971    0.992029
9236445206_R03C02    0.008151    0.991849
9238348151_R04C02    0.00824    0.99176
9236445206_R04C02    0.008581    0.991419
9238348151_R03C01    0.00861    0.99139
9238348151_R01C01    0.009357    0.990643
9238348051_R02C02    0.009463    0.990537
9236442092_R05C01    0.009687    0.990313
9238348012_R05C02    0.00971    0.99029
9238349162_R04C01    0.0101    0.9899
9236445201_R04C01    0.0104    0.9896
9238348151_R04C01    0.01131    0.98869
9238348151_R02C02    0.01141    0.98859
9238348151_R05C02    0.01156    0.98844
9236445201_R01C01    0.01157    0.98843
9238349162_R05C02    0.01228    0.98772
9238349162_R04C02    0.0125    0.9875
9236442092_R05C02    0.01274    0.98726
9238348151_R02C01    0.01309    0.98691
9238348151_R01C02    0.01368    0.98632
9236445201_R01C02    0.01379    0.98621
9236442092_R03C01    0.01403    0.98597
9238348151_R05C01    0.01404    0.98596
9238348012_R04C01    0.01446    0.98554
9238348151_R06C02    0.01483    0.98517
9238348074_R05C01    0.015    0.985
9238349162_R03C02    0.01534    0.98466
9238348120_R03C02    0.01552    0.98448
9238348074_R02C02    0.01564    0.98436
9238348120_R04C02    0.0157    0.9843
9238349162_R02C01    0.01577    0.98423
9238348151_R06C01    0.01583    0.98417
9238348012_R04C02    0.01604    0.98396
9236442092_R04C01    0.01624    0.98376
9236442092_R04C02    0.01653    0.98347
9238348012_R02C02    0.01653    0.98347
9238349162_R05C01    0.01731    0.98269
9238348074_R02C01    0.01804    0.98196
9236442092_R02C01    0.01829    0.98171
9236442092_R06C02    0.01887    0.98113
9238348012_R06C02    0.01893    0.98107
9238348074_R06C01    0.01904    0.98096
9238349162_R02C02    0.01987    0.98013
9238348120_R05C01    0.02015    0.97985
9238349162_R01C01    0.02153    0.97847
9238349162_R06C02    0.02183    0.97817
9238348012_R03C02    0.02187    0.97813
9238348012_R01C02    0.02196    0.97804
9238348120_R03C01    0.02263    0.97737
9238348067_R03C01    0.02268    0.97732
9238349162_R03C01    0.02308    0.97692
9238348074_R01C02    0.02319    0.97681
9236442092_R03C02    0.02322    0.97678
9238348120_R01C01    0.02367    0.97633
9238388100_R01C01    0.0237    0.9763
9238388096_R02C01    0.02381    0.97619
9238388096_R01C01    0.02417    0.97583
9238348012_R03C01    0.02418    0.97582
9236442092_R02C02    0.02684    0.97316
9238348120_R06C02    0.027    0.973
9238348012_R02C01    0.0271    0.9729
9238348074_R03C01    0.02717    0.97283
9238348120_R05C02    0.02726    0.97274
9238348067_R04C01    0.02757    0.97243
9236442092_R01C02    0.02775    0.97225
9238348120_R06C01    0.02781    0.97219
9238348120_R02C01    0.02836    0.97164
9238348074_R06C02    0.02976    0.97024
9238348120_R04C01    0.03011    0.96989
9238349162_R01C02    0.03062    0.96938
9238348074_R04C01    0.0315    0.9685
9238348037_R04C02    0.03189    0.96811
9238348074_R01C01    0.03224    0.96776
9238348051_R04C02    0.0344    0.9656
9238348067_R01C01    0.03537    0.96463
9238388096_R01C02    0.0355    0.9645
9238348067_R02C01    0.03699    0.96301
9238348012_R01C01    0.03703    0.96297
9238388096_R05C02    0.03815    0.96185
9238348074_R03C02    0.03891    0.96109
9238348074_R05C02    0.03902    0.96098
9238348120_R01C02    0.04036    0.95964
9238348120_R02C02    0.04058    0.95942
9238348109_R05C01    0.04138    0.95862
9238388096_R03C02    0.04483    0.95517
9238348083_R05C01    0.04534    0.95466
9238348037_R05C02    0.04574    0.95426
9238348067_R06C02    0.04713    0.95287
9238348067_R05C02    0.04727    0.95273
9236442092_R01C01    0.04804    0.95196
9238348067_R05C01    0.04829    0.95171
9238348037_R05C01    0.04937    0.95063
9238348109_R03C01    0.05044    0.94956
9238348037_R06C01    0.054    0.946
9238348037_R02C02    0.05445    0.94555
9238388096_R04C01    0.05482    0.94518
9238348067_R06C01    0.0557    0.9443
9238388096_R06C02    0.05586    0.94414
9238348067_R04C02    0.05613    0.94387
9238348067_R03C02    0.05848    0.94152
9238388096_R02C02    0.05943    0.94057
9238348067_R01C02    0.06127    0.93873
9238348037_R03C02    0.06182    0.93818
9238348037_R06C02    0.06475    0.93525
9238388096_R05C01    0.07421    0.92579
9238388096_R04C02    0.07871    0.92129
9238348067_R02C02    0.08097    0.91903
9238388096_R03C01    0.08975    0.91025
9238388096_R06C01    0.09201    0.90799
9238348083_R03C01    0.1041    0.8959
9238348037_R01C02    0.1236    0.8764
9238348151_R03C02    0.3272    0.6728
9238348074_R04C02    0.4058    0.5942
9238349162_R06C01    0.5228    0.4772
9236445201_R02C02    0.9997    0.0003
teepean, Dewsloth, corrigendum like this post
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#17
I think I should create a new topic for this but one interesting study that had paper available.

Genotyping of 75 individuals from the Afrikaner population of South Africa

https://pubmed.ncbi.nlm.nih.gov/32089133/

Here's the plink dataset they had in map format that I converted to bed.

https://drive.google.com/drive/folders/1...drive_link
Capsian20, Anglesqueville, corrigendum like this post
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#18
This looks interesting as well.

Genotyping of 323 healthy Europeans blood samples (CEDAR cohort) for cis-eQTL analysis in 6 immune cell types and ileal, colonic and rectal biopsies.

https://www.ebi.ac.uk/biostudies/arrayex...-MTAB-6666

Paper:

https://pubmed.ncbi.nlm.nih.gov/29930244/
Qrts and Capsian20 like this post
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#19
Too bad it's all from the Northern Governorate and not a complete coverage of districts.

There are 9 Governorates in Lebanon with 1-~6 districts in each.
https://en.wikipedia.org/wiki/Districts_of_Lebanon

Mom and her brother have grandparents from Hasbaya District, Keserwan District, Western Beqaa District and Toledo Ohio [Armenia+Beirut?] - each from a different governorate in the southern half of Lebanon.
The Anatolia/Caucasus of the Armenian great-grandparent often bumps them to the overlap of Lebanese Christian and Druze, but on a PCA they both plot close in the core with the center tags for Dinniyeh, Koura and Zgharta, with Batroun not too far way, either.

Distance to: DewslothMom_scaled
0.01758506 Unknown:9238348067_R03C01
0.01935409 Dinniyeh_District:9238349138_R02C01
0.01995828 Koura_District:9238348095_R05C02
0.02053514 Dinniyeh_District:9238348152_R03C01
0.02066800 Zgharta_District:9238388031_R01C02
0.02086738 Zgharta_District:9238348055_R01C02
0.02113631 Dinniyeh_District:9238348055_R02C01
0.02120321 Zgharta_District:9238348049_R05C02
0.02177097 Koura_District:9236445226_R02C01
0.02179831 Koura_District:9238348151_R05C02
0.02190550 Dinniyeh_District:9238348049_R06C02
0.02191307 Zgharta_District:9238348049_R01C02

Distance to: Dewsloth_Uncle_scaled
0.01777805 Unknown:9238348067_R03C01
0.01897777 Koura_District:9238348151_R05C02
0.01939727 Koura_District:9238388096_R04C01
0.01974121 Zgharta_District:9238348083_R01C01
0.01977273 Batroun_District:9238348151_R02C01
0.01992401 Unknown:9238348074_R06C02
0.02001658 Zgharta_District:9238348095_R03C01
0.02024733 Unknown:9238348074_R05C02
0.02074153 Zgharta_District:9238348152_R04C01
0.02109345 Zgharta_District:9236445201_R03C01
0.02122565 Zgharta_District:9236445147_R04C01
0.02135673 Zgharta_District:9238348120_R04C02

Target: DewslothMom_scaled
Distance: 0.6960% / 0.00695980
52.0 Dinniyeh_District
33.6 Zgharta_District
8.6 Koura_District
3.6 Tripoli_District
2.2 Batroun_District

Target: Dewsloth_Uncle_scaled
Distance: 0.6224% / 0.00622355
46.2 Koura_District
38.6 Zgharta_District
9.2 Dinniyeh_District
6.0 Tripoli_District
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R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>FT354149

Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583; John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593; John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635
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#20
(03-31-2024, 01:56 AM)Dewsloth Wrote: Too bad it's all from the Northern Governorate and not a complete coverage of districts.

There are 9 Governorates in Lebanon with 1-~6 districts in each.
https://en.wikipedia.org/wiki/Districts_of_Lebanon

Mom and her brother have grandparents from Hasbaya District, Keserwan District, Western Beqaa District and Toledo Ohio [Armenia+Beirut?] - each from a different governorate in the southern half of Lebanon.
The Anatolia/Caucasus of the Armenian great-grandparent often bumps them to the overlap of Lebanese Christian and Druze, but on a PCA they both plot close in the core with the center tags for Dinniyeh, Koura and Zgharta, with Batroun not too far way, either.

There were some samples that iaap-cli could not convert but from those same districts.

https://support.illumina.com/downloads/i...g-cli.html
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#21
Here's where I found the Lebanese data:

https://www.ebi.ac.uk/biostudies/arrayex...MTAB-13882
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#22
(03-30-2024, 07:26 PM)AimSmall Wrote: Heatmap of samples compared to Davidski's Standard G25

<blockquote class="imgur-embed-pub" lang="en" data-id="a/7rfVmZ2"  ><a href="//imgur.com/a/7rfVmZ2">Genetic Lineages of North Lebanon - Ancient Anatolians to Greek Orthodoxy compared to G25 Standard_heatmap</a></blockquote>

Hello AimSmall
witch tool did you use to make this graph ?
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#23
Any list on the yDNA assignments?
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#24
(04-03-2024, 05:52 AM)Fabrice E Wrote:
(03-30-2024, 07:26 PM)AimSmall Wrote: Heatmap of samples compared to Davidski's Standard G25

Genetic Lineages of North Lebanon - Ancient Anatolians to Greek Orthodoxy compared to G25 Standard_heatmap

Hello AimSmall
witch tool did you use to make this graph ?

R code from Nganasankhan ....

Heatmaps of G25 Euclidean distances with R [Archive] - The Apricity Forum: A European Cultural Community
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#25
(04-03-2024, 02:50 PM)AimSmall Wrote:
(04-03-2024, 05:52 AM)Fabrice E Wrote:
(03-30-2024, 07:26 PM)AimSmall Wrote: Heatmap of samples compared to Davidski's Standard G25

Genetic Lineages of North Lebanon - Ancient Anatolians to Greek Orthodoxy compared to G25 Standard_heatmap

Hello AimSmall
witch tool did you use to make this graph ?

R code from Nganasankhan ....

Heatmaps of G25 Euclidean distances with R [Archive] - The Apricity Forum: A European Cultural Community

Shell commands and R scripts for working with G25 | Genoplot
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#26
(03-31-2024, 07:18 AM)teepean Wrote: Here's where I found the Lebanese data:

https://www.ebi.ac.uk/biostudies/arrayex...MTAB-13882

Quote:Population genetics studies From Ancient Anatolians to Greek Orthodoxy: Genetic Lineages of North Lebanon
The focus of this submission is to genetically identify the population fingerprint of the contemporary population and sub-populations of Northern Lebanon. To this end, the HumanOmniExpress 12 array has been used to comprehensively genotype 344 selected samples from different communities. The samples were collected with careful scrutiny to their heritage, documenting at least two generations of ancestry for each sample.

(04-03-2024, 08:14 AM)Riverman Wrote: Any list on the yDNA assignments?

I would also be interested if the HumanOmniExpress 12 array contains any Y chromosome data?
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#27
(04-30-2024, 01:31 PM)ChrisR Wrote:
(03-31-2024, 07:18 AM)teepean Wrote: Here's where I found the Lebanese data:

https://www.ebi.ac.uk/biostudies/arrayex...MTAB-13882

Quote:Population genetics studies From Ancient Anatolians to Greek Orthodoxy: Genetic Lineages of North Lebanon
The focus of this submission is to genetically identify the population fingerprint of the contemporary population and sub-populations of Northern Lebanon. To this end, the HumanOmniExpress 12 array has been used to comprehensively genotype 344 selected samples from different communities. The samples were collected with careful scrutiny to their heritage, documenting at least two generations of ancestry for each sample.

(04-03-2024, 08:14 AM)Riverman Wrote: Any list on the yDNA assignments?

I would also be interested if the HumanOmniExpress 12 array contains any Y chromosome data?

Looks like it has less than 3000 Y snps.
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#28
To call a paper "genetic lineages" (!) without considering uniparental data is kind of an oxymoron to me.
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