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Thread: Update of a tool for Y-DNA from 23andme

  1. #1
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    Update of a tool for Y-DNA from 23andme

    I updated the 23andMe To YSNPs tool created by Felix and changed the name to 23andMe to ISOGG 2017 Y-SNPs since it now uses the 2017 ISOGG tree from https://isogg.org/tree/2017/index17.html The database only includes the Y-DNA SNPs referenced in the raw DNA files from 23andme. The output is different than the old tool also I included the ancestral and derived alleles, the 2017 ISOGG Longhand name, the mutation, and a note as to whether or not the SNP is tested [by the v5 chip]. I forgot to include that detail in brackets. I removed a small number of SNPs that have shown to be false positives or false negatives.

    The output can be save as a CSV which can then be uploaded here as a text file and can be opened locally with Excel or OpenOffice or by uploading to Google Sheets.

    The program be downloaded from here. Please let me know the results if you try it out.

  2. The Following 2 Users Say Thank You to ArmandoR1b For This Useful Post:

     aaronbee2010 (10-15-2018),  oz (10-16-2018)

  3. #2
    Gold Class Member
    Posts
    1,293
    Sex
    Location
    Birmingham, UK
    Ethnicity
    Indian - Punjabi Jatt
    Nationality
    British
    Y-DNA (P)
    R2-SK2142 > Y1383*
    mtDNA (M)
    U7a3a5a1
    Y-DNA (M)
    R1b-Z2109 > Y84821
    mtDNA (P)
    M5a1a (185G)

    England United Kingdom India Punjab India
    Nice! I'm looking forward to trying this later. 23andMe sucks for R2, but I can see what positive SNPs 23andMe have tested me for nonetheless, as well and get a general idea of how their tree compares to ISOGGs 2017 tree.
    Last edited by aaronbee2010; 10-15-2018 at 06:44 PM.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > Y1383* - M5a1a (185G)
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a5a1
    * MGMs MGF: R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana: T-M70 > Y11151 - R30b1

    Hidden Content

  4. #3
    Gold Class Member
    Posts
    1,293
    Sex
    Location
    Birmingham, UK
    Ethnicity
    Indian - Punjabi Jatt
    Nationality
    British
    Y-DNA (P)
    R2-SK2142 > Y1383*
    mtDNA (M)
    U7a3a5a1
    Y-DNA (M)
    R1b-Z2109 > Y84821
    mtDNA (P)
    M5a1a (185G)

    England United Kingdom India Punjab India
    Here are the positive SNPs I found with your tool. Haplogroups with red text are ones that I'm not descended from, so the SNPs next to them are false positives. Also, it's nice to see that 23andMe haven't tested me for even one SNP downstream of M124, and by nice I mean s**t.

    A0-T: L1101
    A1: P305, V168, V241, V250
    A1b: L989, L1009, L1013
    A1b1b2b: M127
    BT: M42, M94, M9118/Page81, SRY10831.1
    C: CTS7301/M3716/PF2705
    F: M89/PF2746, CTS3654/M3689/PF2667, CTS12632/M3771/PF2775, F719/IMS-JST00305/M3636/S8235, F1209/M3654/YSC0001297, F1329/M3658/PF2622/YSC0001299, F1704/M3675/PF2651, F1753/M3681/PF2658, F2048/M3701/PF2683/V3268, F2075/PF2685, F2155/M3704/PF2690, F2402/M3714/PF2700, F2837/M3726/PF2722, F3111/M3740/PF2736, F3136/M3741/PF2737, L132.1, M3638/PF2590/V205, M3652/PF2615, M3750/PF2747, M3751/PF2748, P14/PF2704, P135/PF2741, P136/PF2762, P138/PF2655, P139, P141/PF2602, P145/PF2617, P148/PF2734, P149, P157, P158/PF2706, P159/PF2717, P160/PF2618, P163, P166/PF2702, PF2608,
    GHIJK: F1329/M3658/PF2622/YSC0001299
    G2a2b2a1a1b1a1a2a2a: F3484.2
    K: M9
    K~: P128/PF5504, P131/PF5493, P132/PF5480
    K2b: M1221/P331/PF5911
    P [K2b2]: P295/PF5866/S8, F91/PF5862/V231
    P~ or K2b2~: CTS196/PF5845, CTS3135/M1206/PF5898, CTS4944/M1218/PF5909, CTS5884/M1228/PF5917, CTS7604/M1235/PF5928, CTS9162/L1185/M1241/PF5937, F29/L821/M5579/PF5857, F332/M1224/PF5914, F359/M1229/PF5920, F524/M1248/PF5945, F640/M1271/PF5975, F671/M1274/PF5981, L82/PF5972, M1109, M1160/PF5958, M1187/PF5865, M1192/PF5872, M1216/PF5908, M1240/PF5936, M1260/PF5957, M1264, PF5982
    P1 [K2b2a]: M45/PF5962, F1857/P337/Page83/PF5901, P226/PF5879, P228/PF5927, P230/PF5925, P235/PF5946, P237/PF5873, P239/PF5930, P243/PF5874, P244/PF5896, P281/PF5941, P282/PF5932, P283/PF5966, P284
    P1~ or K2b2a~: L768/PF5976/YSC0000274
    R [K2b2a2]: M207/Page37/UTY2, CTS3229/M672/PF6036/YSC0001265, F47/M607/Y472, F63/M614/PF6016, F295/M685, F370/M708/Y479, F459/Y482, L747/M702/PF5918/YSC0000287, M734/PF6057/S4/YSC0000201, M760/Y506, M764/PF5953, M799, P224/PF6050, P229/PF6019, P232, P280
    R2: M479/PF6107, L266/PF6108
    R2a: M124, F820/Page4

    I could look at the remaining SNP's I've been tested for (the negative ones) but that would take about a year.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > Y1383* - M5a1a (185G)
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a5a1
    * MGMs MGF: R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana: T-M70 > Y11151 - R30b1

    Hidden Content

  5. #4
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    Quote Originally Posted by aaronbee2010 View Post
    Here are the positive SNPs I found with your tool. Haplogroups with red text are ones that I'm not descended from, so the SNPs next to them are false positives. Also, it's nice to see that 23andMe haven't tested me for even one SNP downstream of M124, and by nice I mean s**t.


    A1b1b2b: M127
    C: CTS7301/M3716/PF2705

    G2a2b2a1a1b1a1a2a2a: F3484.2


    I could look at the remaining SNP's I've been tested for (the negative ones) but that would take about a year.
    All of the kits that I have looked at have G for A1b1b2b: M127 which is negative. What is your Genotype for that SNP?

    Only some of the kits that I have show T for CTS7301/M3716/PF2705 but some do show C. YFull doesn't have CTS7301. I will have to look into that more but it looks like it will have to be removed from the table because not everyone that should get the same result do get the same result.

    All of the kits that I have looked at have G for G2a2b2a1a1b1a1a2a2a: F3484.2 which means they are negative. What is your Genotype for that SNP?

    Will you save the Displayed Table as a CSV and upload it as an attachment here but change the extension to TXT first?

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     aaronbee2010 (10-20-2018)

  7. #5
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    Quote Originally Posted by aaronbee2010 View Post
    ....
    The reference table for CTS7301/M3716/PF2705 had the mutation backwards. I had accidentally changed it once when trying to correct some other data. I fixed the reference table in the tool and the new version should no longer show you positive for CTS7301/M3716/PF2705.

    G2a2b2a1a1b1a1a2a2a: F3484.2 Normally when an SNP has a .2 at the end it is a recurrent or reverse mutation but I couldn't find the other SNP with the same position in my reference table from ISOGG. But Ybrowse has it at http://ybrowse.org/gb2/gbrowse/chrY/? as F3484 and F3484.1 with a note that it is Found in a hg R2 person. Likely a singleton mutation G to A reference Yan Shi (2011) primary id 288882. So congratulations. That is not likely to be a singleton after all.

  8. The Following User Says Thank You to ArmandoR1b For This Useful Post:

     aaronbee2010 (10-20-2018)

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