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Continuation from original GA forum...
Here are additional G25 samples from Davidski and friends...
Quote:Newly Labelled (Matt): https://pastebin.com/Gtj6vEYL
Previously Labelled by NO and newly labelled: https://pastebin.com/RVBaj3RT
--Source: Eurogenes Blog: The Caucasus is a semipermeable barrier to gene flow
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(09-29-2023, 03:46 PM)AimSmall Wrote: Continuation from original GA forum...
Here are additional G25 samples from Davidski and friends...
Quote:Newly Labelled (Matt): https://pastebin.com/Gtj6vEYL
Previously Labelled by NO and newly labelled: https://pastebin.com/RVBaj3RT
--Source: Eurogenes Blog: The Caucasus is a semipermeable barrier to gene flow
Is this just the data from the 2022 pre-print, or has the paper already been published?
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(09-30-2023, 07:06 PM)R.Rocca Wrote: (09-29-2023, 03:46 PM)AimSmall Wrote: Continuation from original GA forum...
Here are additional G25 samples from Davidski and friends...
Quote:Newly Labelled (Matt): https://pastebin.com/Gtj6vEYL
Previously Labelled by NO and newly labelled: https://pastebin.com/RVBaj3RT
--Source: Eurogenes Blog: The Caucasus is a semipermeable barrier to gene flow
Is this just the data from the 2022 pre-print, or has the paper already been published?
Just the data from the preprint. No official publication that I know of.
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Allentoft et al. 2023 120 aDNA samples from "Population Genomics of Stone Age Eurasia" has just been included in FTDNA Discovery tree.
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Does anyone know how many snps Georgia_Kotias_UP:NEO283 had? On a pca it seems to plot closer to North Africans then the ppnb/c samples and the natufian samples including the ana shifted one I0867
Distance to: Son_scaled
0.18580155 Georgia_Kotias_UP:NEO283
0.18736497 Levant_Meoslithic:Levant_Natufian_EpiP:I0861
0.19926438 Levant_Neolithic:Levant_PPNB:I1414
0.20090605 Levant_Neolithic:Levant_PPNB:BAJ001
0.20160385 Levant_Meoslithic:Levant_Natufian_EpiP:I1072
0.20420353 Levant_Neolithic:Levant_PPNB:I1707
0.20755294 Levant_Neolithic:Levant_PPNB:I1700
0.20820925 Levant_Neolithic:Levant_PPNC:I1699
0.20961255 Levant_Neolithic:Levant_PPNC:I1708
0.21299586 Morocco_Iberomaurusian:TAF009_noUDG
0.21594478 Levant_Neolithic:Levant_PPNB:I0867
0.23292824 Levant_Neolithic:Levant_PPNB:I1710
0.24155956 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1103
0.24401398 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1100
0.24416535 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1102
0.24598099 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1098
0.24830547 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1099
0.24874829 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1101
0.24968095 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0745
0.25235559 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0736
0.25408654 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0708
0.25410610 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1581
0.25459779 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1583
0.25531988 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0746
0.25533035 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1585
Distance to: Moroccan_Jebala
0.15020236 Georgia_Kotias_UP:NEO283
0.15275417 Levant_Neolithic:Levant_PPNB:I1414
0.15514273 Levant_Neolithic:Levant_PPNB:BAJ001
0.15855722 Levant_Neolithic:Levant_PPNB:I1700
0.15863801 Levant_Meoslithic:Levant_Natufian_EpiP:I0861
0.16000796 Levant_Neolithic:Levant_PPNC:I1708
0.16093619 Levant_Neolithic:Levant_PPNC:I1699
0.16213473 Levant_Neolithic:Levant_PPNB:I1707
0.16689526 Levant_Neolithic:Levant_PPNB:I0867
0.16824539 Levant_Meoslithic:Levant_Natufian_EpiP:I1072
0.17989811 Levant_Neolithic:Levant_PPNB:I1710
0.18880907 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1103
0.18932676 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1100
0.19107796 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1098
0.19126344 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1102
0.19518586 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1101
0.19536837 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1099
0.19618466 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0736
0.19815019 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0745
0.19935839 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1585
0.20024838 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1581
0.20050902 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1583
0.20240483 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0708
0.20300079 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I1580
0.20328678 Anatolian_Neolithic:TUR_Marmara_Barcin_N:I0854
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10-01-2023, 01:27 AM
(This post was last modified: 10-01-2023, 02:35 AM by AimSmall.)
(10-01-2023, 12:53 AM)Gene188288 Wrote: Does anyone know how many snps Georgia_Kotias_UP:NEO283 had? On a pca it seems to plot closer to North Africans then the ppnb/c samples and the natufian samples including the ana shifted one I0867
I nuked all of my BAM files I created from the FASTQs today as I needed the space back.
However I did keep my statistics files for some reason. I aligned that one to HG38. I don't know what was given to Davidski to make the G25 coordinates, but the true raw data has the following available. It was a high quality sample.
NEO283 snp stats.JPG (Size: 62.16 KB / Downloads: 988)
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Well, that answers that question.... the high coverage I was aligning to was because they imputed the samples to fill in the gaps.
"Using recent advances, we imputed >1,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences."
"To validate imputation, 42 high coverage (5X to 39X) genomes were downsampled for testing (see also Mota et al. submitted1*."
“Our study comprises the largest genomic dataset on European hunter-gatherers to date, including 113 imputed hunter-gatherer genomes of which 79 were sequenced in this study. Among them, we report a 0.83X genome of an Upper Palaeolithic (UP) skeleton from Kotias Klde Cave in Georgia, Caucasus (NEO283), directly dated to 26,052 - 25,323 cal BP (95%). "
(10-01-2023, 01:48 AM)AimSmall Wrote: Well, that answers that question.... the high coverage I was aligning to was because they imputed the samples to fill in the gaps.
"Using recent advances, we imputed >1,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences."
"To validate imputation, 42 high coverage (5X to 39X) genomes were downsampled for testing (see also Mota et al. submitted1*."
“Our study comprises the largest genomic dataset on European hunter-gatherers to date, including 113 imputed hunter-gatherer genomes of which 79 were sequenced in this study. Among them, we report a 0.83X genome of an Upper Palaeolithic (UP) skeleton from Kotias Klde Cave in Georgia, Caucasus (NEO283), directly dated to 26,052 - 25,323 cal BP (95%). "
Thanks for the answer
Hopefully they can do something similar with the other natufian samples, as Davidski said there is not enough data to add them to g25. Because we have some interesting ones that heavily shift towards us
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10-02-2023, 06:01 PM
(This post was last modified: 10-02-2023, 06:22 PM by Kale.)
Just doing a bit of work grouping samples... the ones from the Sakhtish site vary a bit in time, but all of them (that I considered to have decent enough coverage)...
NEO178,179,180,184,185,186,187,189,192,193,195,197
...Pass in qpadm as 100% the highest coverage one (NEO194) with right pops...
right = c('Congo_Mbuti.DG', 'Taforalt', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'Anatolia_Barcin_N.SG', 'Anatolia_Boncuklu_N.SG', 'Iran_Wezmeh_N.SG', 'Iran_GanjDareh_N', 'CHG.SG', 'Italy_GrottaContinenza_HG.SG', 'Ireland_Sramore_HG.SG', 'RUS_Arkhangelsk_HG.SG', 'RUS_Vologda_Minino_HG', 'Afanasievo_KarasukIII.SG', 'Yamnaya_Kazakhstan_Karagash.SG', 'Botai.SG', 'Tarim_EMBA1', 'RUS_Primorsky_DevilsCave_N.SG', 'RUS_Irkutsk_Shamanka_EN.SG', 'Peru_RioUncallane_1800BP.SG', 'Bahamas_SouthAndros_Ceramic.SG')
Same with Vasilyevskiy samples...
NEO160,163,164,167,170,171
Passing as the highest coverage, NEO166.
NEO162 appears damaged/contaminated.
NEO283 (Kotias_UP) groups with Dzudzuana (S2949) with right...
right = c('Congo_Mbuti.DG', 'Taforalt', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'China_UP', 'Kostenki14', 'Muierii1', 'Sunghir.SG', 'Gravettian_KremsVestonice', 'BachoKiro_BK1653', 'GoyetQ116_1', 'Yana_UP.SG', 'MA1.SG', 'Anatolia_Barcin_N.SG', 'Iran_Wezmeh_N.SG', 'CHG.SG', 'Italy_GrottaContinenza_HG.SG', 'RUS_Arkhangelsk_HG.SG', 'RUS_Primorsky_DevilsCave_N.SG', 'Peru_RioUncallane_1800BP.SG')
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Vladimir over at Eurogenes said...
Quote:The Allentoft base appears to have expanded again. It added 32 more samples that are not on your G25 list. This: NEO1, NEO3, NEO7, NEO13, NEO41, NEO61, NEO76, NEO102, NEO223, NEO496, NEO514, NEO545, NEO549, NEO550, NEO553, NEO566, NEO568, NEO571, NEO580, NEO795, NEO817, NEO857, NEO915, NEO938, NEO941, NEO942, NEO945, NEO946, NEO951, NEO960, NEO961, NEO962.
https://www.ebi.ac.uk/ena/browser/view/PRJEB64656
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(10-04-2023, 04:32 PM)R.Rocca Wrote: Vladimir over at Eurogenes said...
Quote:The Allentoft base appears to have expanded again. It added 32 more samples that are not on your G25 list. This: NEO1, NEO3, NEO7, NEO13, NEO41, NEO61, NEO76, NEO102, NEO223, NEO496, NEO514, NEO545, NEO549, NEO550, NEO553, NEO566, NEO568, NEO571, NEO580, NEO795, NEO817, NEO857, NEO915, NEO938, NEO941, NEO942, NEO945, NEO946, NEO951, NEO960, NEO961, NEO962.
https://www.ebi.ac.uk/ena/browser/view/PRJEB64656
I don't like begging, but on the other hand, I like reading BAM files even less. I hope that when the PLINK file has been updated a link will be posted here.
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NEO538 is still not available? The sample is N-Z1936, just like the ST sample ROT02 of Rostovka, however NEO538 was found in Vologda area and it is younger, something like late BA/early IA, if I'm right.
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Does anyone have the genotype data of those last 100 individuals yet?
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(10-11-2023, 09:17 PM)schnurkeramik Wrote: I'm still aligning these
https://docs.google.com/spreadsheets/d/1...sp=sharing
Still aligning?
Are you using pileupCaller by chance?
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