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Thread: France Iron Age references average.

  1. #11
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    Quote Originally Posted by anglesqueville View Post
    FRA_IA ATT26 N 1117397 1200343 0.9309
    FRA_IA BES1248 N 1099261 1200343 0.9158
    FRA_IA BFM265 N 1065095 1200343 0.8873
    FRA_IA COL11 N 1111186 1200343 0.9257
    FRA_IA COL153A N 1105007 1200343 0.9206
    FRA_IA COL153i N 1132205 1200343 0.9432
    FRA_IA ERS86 N 1082183 1200343 0.9016
    FRA_IA ERS88 N 1115725 1200343 0.9295
    FRA_IA ERS1164 N 1073601 1200343 0.8944
    FRA_IA Jeb8 N 1113748 1200343 0.9279
    FRA_IA NOR3-6 N 1094826 1200343 0.9121
    FRA_IA NOR3-15 N 1120517 1200343 0.9335
    FRA_IA NOR4 N 1125648 1200343 0.9378
    FRA_IA PECH5 N 1162208 1200343 0.9682
    FRA_IA PEY53 N 1105845 1200343 0.9213

    The last number is the percentage of no-calls. Just think.

    edit: the reference basis of these stats is the 1240K of Reich.
    Anglesqueville, do you know why the following samples (PEY163, PECH5, PT2, PECH8) are not on the G25 btw ? The study had 19 Iron age samples, and we only have 15 on the G25, the 4 missing are the ones I mentioned and from Languedoc ?

    Sans titre.png

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  3. #12
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    Quote Originally Posted by jstephan View Post
    Anglesqueville, do you know why the following samples (PEY163, PECH5, PT2, PECH8) are not on the G25 btw ? The study had 19 Iron age samples, and we only have 15 on the G25, the 4 missing are the ones I mentioned and from Languedoc ?

    Sans titre.png
    PECH5 is, among the ones we have on the PLINK-file, the lowest coverage (nearly 97% of no-calls). I guess that the three others are even worse.
    En North alom, de North venom
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  5. #13
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    Quote Originally Posted by anglesqueville View Post
    PECH5 is, among the ones we have on the PLINK-file, the lowest coverage (nearly 97% of no-calls). I guess that the three others are even worse.
    Which is usually the % needed of no-calls for a sample to be considered non valid or low confidence one? Is there any convention about this?

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  7. #14
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    No need of convention, only common sense. Would you buy analysis from a company who would genotype only 100.000 SNPs, and even not guaranteed because of possible errors? Furthermore, in the case of aDNA, we should take into account the deamination. In particular, if you want to compare these IA genomes to modern ones the good practice is to keep only transversions. How many transversions do remain from their 100.000 - 150.000 SNPs? Answer: make the difference between the two first columns.

    FRA_IA ATT26 N 247675 262757 0.9426
    FRA_IA BES1248 N 244142 262757 0.9292
    FRA_IA BFM265 N 237923 262757 0.9055
    FRA_BA BIS130 N 245189 262757 0.9331
    FRA_BA BIS385 N 239798 262757 0.9126
    FRA_BBC CBV95 N 242771 262757 0.9239
    FRA_IA COL11 N 246390 262757 0.9377
    FRA_IA COL153A N 245367 262757 0.9338
    FRA_IA COL153i N 250658 262757 0.954
    FRA_IA ERS86 N 241481 262757 0.919
    FRA_IA ERS88 N 247475 262757 0.9418
    FRA_IA ERS1164 N 239775 262757 0.9125
    FRA_BA EUG11 N 242130 262757 0.9215
    FRA_IA Jeb8 N 247153 262757 0.9406
    FRA_BA NIED N 247038 262757 0.9402
    FRA_IA NOR2B6 N 238122 262757 0.9062
    FRA_IA NOR3-6 N 243552 262757 0.9269
    FRA_IA NOR3-15 N 248301 262757 0.945
    FRA_IA NOR4 N 249062 262757 0.9479
    FRA_BA OBE3626-1 N 229611 262757 0.8739
    FRA_BA OBE3722 N 239553 262757 0.9117
    FRA_IA PECH5 N 255736 262757 0.9733
    FRA_IA PEY53 N 245537 262757 0.9345

    No, really, forget these Iron Age ghosts. We all have to wait for samples resulting from really professional work and avoid making farfetched discourses about genomes that so far don't exist.
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  9. #15
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    Quote Originally Posted by anglesqueville View Post

    No, really, forget these Iron Age ghosts. We all have to wait for samples resulting from really professional work and avoid making farfetched discourses about genomes that so far don't exist.
    Ce que vous avez dit encourage encore plus ma curiosité.

    C'est comme quand vous dites à un enfant "ne joue pas avec ça, ne touche pas à ça, n'entre pas là-dedans".

    Et en plus de cela, j'aime perdre mon temps avec des choses inutiles.

    Même si je ne vois pas grand chose d'autre à faire avec ces références. Au moins pour le moment.

  10. #16
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    Yes, it is human, and after all, we are only humble "amateurs". But even amateurs should be keen to respect the minimum of scientific rigour, even when some professionals forget it. The scandalous poverty of the specimens sequenced by Brunel for her thesis and the Ancestra project has been for all of us, who have been waiting for them for so long, a source of frustration and anger. But after all, it wasn't the first time. I have, for a lot of reasons, an interest at least as great for Fennoscandian genetics as for French genetics. When the first Estonian Iron Age genomes were published by Saag in 2019, I experienced a similar disappointment, as most genomes had poor coverage at best, and some were downright unusable. But there you go, that's life. G25 aficionados should never forget that behind the 25 components are genomes and that only these genomes are reality.
    En North alom, de North venom
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  12. #17
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    Quote Originally Posted by anglesqueville View Post
    Yes, it is human, and after all, we are only humble "amateurs". But even amateurs should be keen to respect the minimum of scientific rigour, even when some professionals forget it. The scandalous poverty of the specimens sequenced by Brunel for her thesis and the Ancestra project has been for all of us, who have been waiting for them for so long, a source of frustration and anger. But after all, it wasn't the first time. I have, for a lot of reasons, an interest at least as great for Fennoscandian genetics as for French genetics. When the first Estonian Iron Age genomes were published by Saag in 2019, I experienced a similar disappointment, as most genomes had poor coverage at best, and some were downright unusable. But there you go, that's life. G25 aficionados should never forget that behind the 25 components are genomes and that only these genomes are reality.
    In our hands it´s a toy, don´t take it so seriously.

    They will improve samples soon, with new means and methods to extract and analyze Dna from ancient individuals.

  13. #18
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    Quote Originally Posted by mokordo View Post
    In our hands it´s a toy, don´t take it so seriously.

    They will improve samples soon, with new means and methods to extract and analyze Dna from ancient individuals.
    Without a stake, a game quickly becomes boring. The higher the stake, the more the game tends to become a fight. Which stake is more important than the truth?
    En North alom, de North venom
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    Just a detail: those FRA_IA are NOT in the official G25-spreadsheet (I just verified). I believe there are good reasons for that.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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