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Thread: 23andme V5 SNP Coverage

  1. #1
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    23andme V5 SNP Coverage

    Recently I have purchased a 23andm3 kit, and while the results it shows me look good considering my ancestry, when I uploaded the raw data to gedmatch very little SNP's were recognized. For example, Eurogenes k13 shows only 60k snp's in comparison to my FTDNA data which shows around 180k. Why is there such a large difference? I can tell that the results look a bit noisy as well, especially on the calcs that by default use lower snp's. This is very frustrating. Does anyone know whether future updates of any kind will fix this issue?

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     Nino90 (02-19-2019)

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    Sorry to say it won't be fixed. And the other testing services will start suffering this fate too. Illumina, the company that makes the beadchip reader system is standardizing to a reduced SNP chip. It's the reason I went and found a company, gencove, that does actual sequencing instead of the chip.

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     Sorcelow (02-08-2018)

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    Quote Originally Posted by therrien.joel View Post
    Sorry to say it won't be fixed. And the other testing services will start suffering this fate too. Illumina, the company that makes the beadchip reader system is standardizing to a reduced SNP chip. It's the reason I went and found a company, gencove, that does actual sequencing instead of the chip.
    Very frustrating, how are the gencove results?

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    Pretty good. In terms of doing matches with kits, it's working just as good as my v4 23andMe kit. The one catch is that as a low coverage sequence, it does not get every last base-pair. So they do use imputing. But they are at least starting with ~10M SNPs vs the 500k from the beadchip system. I have noticed that this ends up with admixtures that seem too clean; there are very few instances of those fractional percents pin the populations.

    Considering that it only costs $60, I can't complain at all!

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    Quote Originally Posted by therrien.joel View Post
    Pretty good. In terms of doing matches with kits, it's working just as good as my v4 23andMe kit. The one catch is that as a low coverage sequence, it does not get every last base-pair. So they do use imputing. But they are at least starting with ~10M SNPs vs the 500k from the beadchip system. I have noticed that this ends up with admixtures that seem too clean; there are very few instances of those fractional percents pin the populations.

    Considering that it only costs $60, I can't complain at all!
    Wait, I'm not sure I understand this but want to know what you're saying... How many SNPs does the Gencove test analyze??
    Last edited by sktibo; 02-08-2018 at 09:09 PM.
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Eastern European and Eastern German (Galicia, Poland) 25%, Scottish 17.96%, Scotch-Irish 12.5%, French 8.2%, Native American 1.95%, and Colonial American, 3.125%, which cannot be determined with complete certainty: there is Dutch (at least 1.36%) and some English. The rest could include Spanish, Norwegian, German, and French, but these percentages would be minuscule.

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    SNPs may be the wrong term here, since this is sequencing, not tagging specific locations on the genome. So, I should say they detect around 10 million base pairs and then use imputation to bring the total up to about 35 million. This ensures that they capture pretty much any SNP that the other commercial test companies test. In other words, my Gedmatch matches with this data are really good

    We also confirmed that this does cover the Y as well. Still haven't figured out if the mtDNA is in there or not.

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    Is anyone else here dissatisfied with their V5 results?

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    Hi all. New here.
    I am looking to compare different SNPs offered by different providers. I am willing to share the results with all of you. Could anyone pleeeease upload their 23andme v5 chip raw data - just the RSs? If you copy-paste all data from the txt file into Excel (or Google sheet) it will automatically put the rs on one column, genes on another, and your personal results on a third. Just delete your results and leave the rest in.

    Thank you in advance to anyone willing to do this

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    How is autosomal matching for genealogical purposes going to be affected with the Illumina GSA chip? I've already had a situation where my Ancestry V1 results would not match with a person on Gedmatch who tested with 23andme V5. A cousin also didn't match with their Ancestry results but also tested with 23andme v5 and had both matches at Genesis.gedmatch. The 23andme v5 test did match. This was enough to for me to get tested at 23andme so that my kits at Gedmatch would have the required SNP coverage to match these newer tests. 23andme and Living DNA are using this test. Will the other testing companies eventually move to the same chip? Should I test my older relatives with this GSA chip before it's too late?

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    difference is quite BIG

    my FTDNA K15

    1 Serbian 3.96
    2 Romanian 4.98
    3 Moldavian 5.94
    4 Bulgarian 7.08
    5 Croatian 7.42

    my 23andMe K15

    1 Romanian 5.57
    2 Bulgarian 6.45
    3 Serbian 6.53
    4 Moldavian 6.79
    5 Croatian 8.85
    Hidden Content
    [/B]
    Modern:
     
    1 Serbian 3.11
    2 Romanian 5.37
    3 Moldavian 6.46
    4 Bulgarian 7.42
    5 Croatian 8.75

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