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***AimSmall*** · (This post was last modified: 03-30-2024, 10:14 PM by AimSmall.)

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 · 03-30-2024, 10:28 PM

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

teepean · 03-30-2024, 10:34 PM

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/

Dewsloth · (This post was last modified: 03-31-2024, 02:04 AM by Dewsloth.)

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

teepean · 03-31-2024, 06:39 AM

(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

teepean · 03-31-2024, 07:18 AM

Here's where I found the Lebanese data:

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

Fabrice E · 04-03-2024, 05:52 AM

(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 ?

Riverman · 04-03-2024, 08:14 AM

Any list on the yDNA assignments?

***AimSmall*** · (This post was last modified: 04-03-2024, 03:35 PM by AimSmall.)

(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

***AimSmall*** · (This post was last modified: 04-03-2024, 03:35 PM by AimSmall.)

(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

ChrisR · 04-30-2024, 01:31 PM

(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?

teepean · 04-30-2024, 02:46 PM

(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.

Riverman · 04-30-2024, 03:22 PM

To call a paper "genetic lineages" (!) without considering uniparental data is kind of an oxymoron to me.

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