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Thread: Methodology of determining new Full Genomes YSNPs - P312/L21

  1. #11
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    Ray

    Thanks. I agree, but I still would have thought that we may have turned up SNPs above Z253 as well.

    I only have the raw data for the PF825+ kit and so have compared its SNPs with the information Robert Casey has posted online about his own results, rather than his raw data. The information with the FG results cautions that only SNP results with at least 95% reliability should be regarded as significant.

    I have forwarded a copy of the PF825+ kit raw SNP data to Robert Casey, with the permission of the kit's owner. I could check if he is happy for me to send you a copy as well if you like. Hopefully it won't be too long before you receive your own FG results, and I think the more people working on comparisons the better.

    We also have a Chromo 2.0 result (positive SNPs only, not raw data) for a different PF825 kit online in the L21 Yahoo Group, so adding those results into the comparison may clarify things further. The kit is Buchanan 200481.

    Greg H

  2. #12
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    Quote Originally Posted by hoxgi View Post
    Ray

    Thanks. I agree, but I still would have thought that we may have turned up SNPs above Z253 as well.



    I have forwarded a copy of the PF825+ kit raw SNP data to Robert Casey, with the permission of the kit's owner. I could check if he is happy for me to send you a copy as well if you like. Hopefully it won't be too long before you receive your own FG results, and I think the more people working on comparisons the better.

    We also have a Chromo 2.0 result (positive SNPs only, not raw data) for a different PF825 kit online in the L21 Yahoo Group, so adding those results into the comparison may clarify things further. The kit is Buchanan 200481.

    Greg H
    Greg,

    That would be great. PF825 and my cluster (253-1716-11) share some common off-modal STR mutations and it is possible that we share some common SNPs downstream of Z253. It would be good to do some comparisons to confirm where they branched when I eventually receive results (batch # 5)

    Ray

  3. #13
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    The Z253/DF825 sponsor received updated results. We now share 20 or 30 shared high quality YSNPs since his original file had no FGC assignments for shared YSNPs or indels like mine did. For now, I think we need to use the Ychr position to find L21 relevant YSNPs since there are many high quality YSNPs with no FGC designations. As we get FGC mapping to YChr, we can replace the YChr designation with the FGC assignments. Also, I only look at high quality mutations blank and *. With at least 50 of these per test, I think we should only concentrate on high quality YSNPs for now. Also, I do plan to review all high quality indels as well.

  4. #14
    Junior Member Peter M's Avatar
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    Quote Originally Posted by RobertCasey View Post
    At this point in time, I am only in analysis mode and attempting to figure out how the test results should be summarized and filtered. I will eventually expand my database to include L21 specific YSNPs. Also, CROMO2 and Krahn's testing results also need to be tracked - this would be too much to expect David to continue expand his scope. No telling how the Big Y results will come in as well. I think we need to split up different testing companies and then share results between those who actually track this kind of data.
    If you want my opinion: do *NOT* split up your activities on the basis of the testing companies the results were obtained from. Focus on a branch of the tree with a width you can handle and then combine ALL results from ALL testing companies for people in that branch. Otherwise I'm afraid you'll find yourself in a big mess shortly.

  5. #15
    Senior Member GoldenHind's Avatar
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    Can anyone tell me anything about CTS11707 and Z6427. I don't see them listed in the ISOGG index of SNPs.

  6. #16
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    Here is the analysis of the Compare files of the P312/DF99, Z253/L226 and Z253/DF825 files:

    Here are some observations:

    1) There are a lot of private high quality YSNPs for each submission.
    2) There seems to be too few YSNPs between Z253 and P312 (labeled Approx Z253).
    3) FGC164 appears to be the best find - between Z253 and P312.
    4) Need to research other approx Z253 candidates, PF5888 and Z252.
    5) All other YSNPs were either all three positive or all three negative.
    6) The PF825 submission also has FGC28 and FGC187 (which are probably one of the five unknown PF825 YSNPs)
    7) I have not received the updated PF825 results - had to cross reference them by YChr positions with L226 results.
    8) YSNPs labeled FSS are high quality FGC Shared SNPs with no known assigned FGC numbers.

    Look forward to comments - will update as I research interesting YSNPs on the list.

    Part 1 of 3 (table was too big for one post):

    aaAnalysis aaP312/DF99 aaZ253/L226 aaZ253/PF825
    Approx DF99 FGC846+ Missing Missing
    Approx DF99 FGC847+ Missing Missing
    Approx DF99 FGC848+ Missing Missing
    Approx DF99 FGC849+ Missing Missing
    Approx DF99 FGC850+ Missing Missing
    Approx DF99 FGC851+ Missing Missing
    Approx DF99 FGC852+ Missing Missing
    Approx DF99 FGC853+ Missing Missing
    Approx DF99 FGC854+ Missing Missing
    Approx DF99 FGC855+ Missing Missing
    Approx DF99 FGC856+ Missing Missing
    Approx DF99 FGC857+ Missing Missing
    Approx DF99 FGC858+ Missing Missing
    Approx DF99 FGC859+ Missing Missing
    Approx DF99 FGC860+ Missing Missing
    Approx DF99 FGC861+ Missing Missing
    Approx DF99 FGC862+ Missing Missing
    Approx DF99 FGC863+ Missing Missing
    Approx DF99 FGC864+ Missing Missing
    Approx DF99 FGC865+ Missing Missing
    Approx DF99 FGC866+ Missing Missing
    Approx DF99 FGC867+ Missing Missing
    Approx DF99 FGC868+ Missing Missing
    Approx DF99 FGC869+ Missing Missing
    Approx DF99 FGC870+ Missing Missing
    Approx DF99 FGC871+ Missing Missing
    Approx DF99 FGC872+ Missing Missing
    Approx DF99 FGC873+ Missing Missing
    Approx DF99 FGC874+ Missing Missing
    Approx DF99 FGC875+ Missing Missing
    Approx DF99 FGC876+ Missing Missing
    Approx DF99 FGC877+ Missing Missing
    Approx DF99 FGC878+ Missing Missing
    Approx DF99 FGC879+ Missing Missing
    Approx DF99 FGC880+ Missing Missing
    Approx DF99 FGC881+ Missing Missing
    Approx DF99 FGC882+; site of CTS9213 Missing Missing
    Approx DF99 FGC883+ Missing Missing
    Approx DF99 FGC884+ Missing Missing
    Approx DF99 FGC885+ Missing Missing
    Approx DF99 FGC886+ Missing Missing
    Approx DF99 FGC887+ Missing Missing
    Approx DF99 FGC888+ Missing Missing
    Approx DF99 FGC889+ Missing Missing
    Approx DF99 FGC890+ Missing Missing
    Approx DF99 FGC891+ Missing Missing
    Approx DF99 FGC892+ Missing Missing
    Approx DF99 FGC893+ Missing Missing
    Approx DF99 FGC894+ Missing Missing
    Approx DF99 FGC895+ Missing Missing
    Approx DF99 FGC896+ Missing Missing
    Approx DF99 FGC897+ Missing Missing
    Approx DF99 FGC898+ Missing Missing
    Approx DF99 FGC899+ Missing Missing
    Last edited by RobertCasey; 12-04-2013 at 04:41 AM.

  7. #17
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    Part 2 of 3:
    Approx L226 Missing FGC1556+ Missing
    Approx L226 Missing FGC1557+ Missing
    Approx L226 Missing FGC267+ Missing
    Approx L226 Missing FGC271+ Missing
    Approx L226 Missing FGC385+ Missing
    Approx L226 Missing FGC498+ Missing
    Approx L226 Missing FGC5618+ Missing
    Approx L226 Missing FGC5619+ Missing
    Approx L226 Missing FGC5620+ Missing
    Approx L226 Missing FGC5621+ Missing
    Approx L226 Missing FGC5622+ Missing
    Approx L226 Missing FGC5623+ Missing
    Approx L226 Missing FGC5624+ Missing
    Approx L226 Missing FGC5625+ Missing
    Approx L226 Missing FGC5626+ Missing
    Approx L226 Missing FGC5627+ Missing
    Approx L226 Missing FGC5628+ Missing
    Approx L226 Missing FGC5629+ Missing
    Approx L226 Missing FGC5630+ Missing
    Approx L226 Missing FGC5631+ Missing
    Approx L226 Missing FGC5632+ Missing
    Approx L226 Missing FGC5633+ Missing
    Approx L226 Missing FGC5634+ Missing
    Approx L226 Missing FGC5635+ Missing
    Approx L226 Missing FGC5636+ Missing
    Approx L226 Missing FGC5637+ Missing
    Approx L226 Missing FGC5638+ Missing
    Approx L226 Missing FGC5639+ Missing
    Approx L226 Missing FGC5640+ Missing
    Approx L226 Missing FGC5641+ Missing
    Approx L226 Missing FGC5642+ Missing
    Approx L226 Missing FGC5643+ Missing
    Approx L226 Missing FGC5644+ Missing
    Approx L226 Missing FGC5645+ Missing
    Approx L226 Missing FGC5646+ Missing
    Approx L226 Missing FGC5647+ Missing
    Approx L226 Missing FGC5648+ Missing
    Approx L226 Missing FGC5649+ Missing
    Approx L226 Missing FGC5650+ Missing
    Approx L226 Missing FGC5651+ Missing
    Approx L226 Missing FGC5652+ Missing
    Approx L226 Missing FGC5653+ Missing
    Approx L226 Missing FGC5654+ Missing
    Approx L226 Missing FGC5655+ Missing
    Approx L226 Missing FGC5656+ Missing
    Approx L226 Missing FGC5657+ Missing
    Approx L226 Missing FGC5658+ Missing
    Approx L226 Missing FGC5659+ Missing
    Approx L226 Missing FGC5660+ Missing

  8. #18
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    Part 3 of 3:

    Approx PF825 Missing Missing FGC3221+
    Approx PF825 Missing Missing FGC3222+
    Approx PF825 Missing Missing FGC3223+
    Approx PF825 Missing Missing FGC3224+
    Approx PF825 Missing Missing FGC3225+
    Approx PF825 Missing Missing FGC3226+
    Approx PF825 Missing Missing FGC3227+
    Approx PF825 Missing Missing FGC3228+
    Approx PF825 Missing Missing FGC3229+
    Approx PF825 Missing Missing FGC3230+
    Approx PF825 Missing Missing FGC3231+
    Approx PF825 Missing Missing FGC3232+
    Approx PF825 Missing Missing FGC3233+
    Approx PF825 Missing Missing FGC3234+
    Approx PF825 Missing Missing FGC3235+
    Approx PF825 Missing Missing FGC3236+
    Approx PF825 Missing Missing FGC3237+
    Approx PF825 Missing Missing FGC3238+
    Approx PF825 Missing Missing FGC3239+
    Approx PF825 Missing Missing FGC3240+
    Approx PF825 Missing Missing FGC3241+
    Approx PF825 Missing Missing FGC3242+
    Approx PF825 Missing Missing FGC3243+
    Approx PF825 Missing Missing FGC3244+
    Approx PF825 Missing Missing FGC3245+
    Approx PF825 Missing Missing FGC3246+
    Approx PF825 Missing Missing FGC3247+
    Approx PF825 Missing Missing FGC3248+
    Approx PF825 Missing Missing FGC3249+
    Approx PF825 Missing Missing FGC3250+
    Approx PF825 Missing Missing FGC3251+
    Approx PF825 Missing Missing FGC3252+
    Approx PF825 Missing Missing FGC3253+
    Approx PF825 Missing Missing FGC3254+
    Approx PF825 Missing Missing FGC3255+
    Approx PF825 Missing Missing FGC3256+
    Approx PF825 Missing Missing FGC3257+
    Approx PF825 Missing Missing FGC3258+
    Approx PF825 Missing Missing FGC3259+
    Approx PF825 Missing Missing FGC3260+
    Approx PF825 Missing Missing FGC3261+
    Approx PF825 Missing Missing FGC3262+
    Approx PF825 Missing Missing FGC3263+
    Approx PF825 Missing Missing FGC3264+
    Approx PF825 Missing Missing FGC3265+
    Approx PF825 Missing Missing FGC3266+
    Approx PF825 Missing Missing FGC3267+
    Approx PF825 Missing Missing FGC3268+
    Approx PF825 Missing Missing FGC3269+
    Approx PF825 Missing Missing FGC3270+
    Approx PF825 Missing Missing FGC3271+
    Approx PF825 Missing Missing FGC3219+
    Approx PF825 Missing Missing FGC3220+
    Approx PF825 Missing Missing FGC187+
    Approx PF825 Missing Missing FGC28+
    Approx PF825 Missing Missing FGC3218+
    Approx Z253 Missing FGC164+ FGC164+
    Approx Z253 Missing PF5888+ PF5888+
    Approx Z253 Missing Z252+ (also known as S471) Z252+ (also known as S471)
    Equiv DF13 Missing Z2542+ (also known as CTS8221) Z2542+ (also known as CTS8221)
    Equiv L21 Missing L459+ Missing
    Equiv L21 Missing Z245+ Z245+
    Equiv L21 Missing Z260+ Z260+
    Equiv L21 Missing Z290+ Z290+
    Inconclusive Missing Missing L116- (also known as S284, PF2955)
    Inconclusive L20- (also known as S144) Missing L20- (also known as S144)
    Inconclusive M2693- (also known as PF5501) Missing Missing
    Inconclusive Missing Missing M9194-
    Inconclusive U2- (also known as S314, PF2952) U2- (also known as S314, PF2952) Missing
    Pre P312 FGC173+ FGC173+ Missing
    Pre P312 CTS3075+ Missing CTS3075+
    Pre P312 FGC148+ FGC148+ Missing
    Pre P312 M1206+ (also known as PF5898, CTS3135) Missing M1206+ (also known as PF5898, CTS3135)
    Same L226 Missing S168+ (also known as L226) Missing
    Same Z253 Missing S218+ (also known as Z253) S218+ (also known as Z253)
    Son L21 Missing DF13+ (also known as S521, CTS241) DF13+ (also known as S521, CTS241)
    Son P312 Missing L21+ (also known as S145, M529) L21+ (also known as S145, M529)
    Son Z253 Missing Z2534+ Missing
    Last edited by RobertCasey; 12-05-2013 at 01:36 AM.

  9. #19
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    I went back and added information from the gtype files and found that the Compare file is just not very reliable for non-FGC YSNPs. I think that the Compare file is the only source for FGC YSNPs and the gtype file is the most reliable source for non-FGC YSNPs.

    All Negative L116- (gtype) L116 - (gtype) L116- (also known as S284, PF2955)
    All Negative L20- (also known as S144) L20 - (gtype) L20- (also known as S144)
    All Negative U2- (also known as S314, PF2952) U2- (also known as S314, PF2952) U2- (gtype)
    All Positive PF5888+ (gtype) PF5888+ PF5888+
    All Positive CTS3075+ CTS3075+ (gtype) CTS3075+
    All Positive M1206+ (also known as PF5898, CTS3135) M1206+ (gtype) M1206+ (also known as PF5898, CTS3135)
    Approx Z253 Missing FGC164+ FGC164+
    Approx Z253 Z252- (gtype) Z252+ (also known as S471) Z252+ (also known as S471)
    Approx Z253 M2693- (also known as PF5501) M2693+ (gtype) M2693+ (gtype)
    Equiv DF13 Z2542- (gtype) Z2542+ (also known as CTS8221) Z2542+ (also known as CTS8221)
    Equiv L21 L459- (gtype) L459+ L459+ (gtype)
    Equiv L21 Z245- (gtype) Z245+ Z245+
    Equiv L21 Z260- (gtype) Z260+ Z260+
    Equiv L21 Z290- (gtype) Z290+ Z290+
    Pre P312 M9194+ (gtype) M9194+ (gtype) M9194-
    Pre P312 FGC173+ FGC173+ Missing
    Pre P312 FGC148+ FGC148+ Missing
    Same L226 S168- (gtype) S168+ (also known as L226) S168- (gtype)
    Same Z253 S218- (gtype) S218+ (also known as Z253) S218+ (also known as Z253)
    Son L21 DF13- (gtype) DF13+ (also known as S521, CTS241) DF13+ (also known as S521, CTS241)
    Son P312 L21- (gtype) L21+ (also known as S145, M529) L21+ (also known as S145, M529)
    Son Z253 Z2534- (gtype) Z2534+ Z2534- (gtype)

  10. #20
    Senior Member MJost's Avatar
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    Robert,

    I have a Excel VB Script that preps a Haplogroup compare file allowing to be merged into the current combined list I have, all with some manual steps prior and post run steps. With four kits merged I am, I have over 2600 positions now. I am trying to get all the tesed L21 subclades included.

    Does DaveR have a complete HaplotypeCompare Out file available?

    MJost
    f148326, FGC-0FW1R, YSeq-ID6. R-DF13>FGC5496>*5521>*5539>*5538>*5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF appears to be from the same Watterson line via Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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