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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
corrigendum, Dewsloth, teepean 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/
Capsian20 and Qrts 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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