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RobertCasey
09-30-2014, 10:47 PM
I am trying to determine how to interpret four YSNPs that I had tested at YSEQ
for private YSNPs under L226 for FTDNA ID 131349 (Casey):


















































62


FGC5618


A+

ChrY

2813045

2813045

62_FGC5618_trA_Plate_Plate01_C0|953

2014-03-27 22:56:09

7225355

1



62

FGC5658

T-

ChrY

28592595

28592595

62_FGC5658ni_trA_Plate_Plate01_|954

2014-03-27 22:57:21

7225356

1

















62


FGC498


G-

ChrY

15659870


15659870

62_Req6_A02_FGC498_trA_A06.ab1|443


2014-09-22 10:10:47

7237268

1

















62


FGC5626

T+

ChrY

7289101

7289101

62_Req6_C02_FGC5626_trA_C06.ab1|445

2014-01-22 01:31:10

7223994

1





























According YSEQ:

FGC498 - Ancestral = G, Derived = A - Results reported above show G- does this equate to Derived A, FGC498+
FGC5618 - Ancestral = C, Derived = A - Results reported above show A+ does this equate to Derived A, FGC5618+
FGC5626 - Ancestral = A, Derived = T - Results reported above show T+ does this equate to Derived T, FGC5626+
FGC5658 - Ancestral = T, Derived = C - Results reported above show T- does this equate to Derived C, FGC5628+

Thanks in advance. I beginning to question this interpretation due to conflicting results.

hoxgi
10-01-2014, 01:19 AM
Robert, I had thought that the minus sign meant that the person is negative for the mutation being tested, and the plus sign means that the mutation is present. So G- means an ancestral result (G allele), negative for mutation (-). Does this interpretation give you more consistency with your results? Perhaps Thomas or Astrid could comment.
Greg H

RobertCasey
10-01-2014, 04:28 AM
I sent an email to YSEQ around one week ago with no response to date. This would then be your interpretation:

FGC498 - Ancestral = G, Derived = A - Results reported above show G- does this equate to Ancestral A, FGC498-
FGC5618 - Ancestral = C, Derived = A - Results reported above show A+ does this equate to Derived A, FGC5618+
FGC5626 - Ancestral = A, Derived = T - Results reported above show T+ does this equate to Derived T, FGC5626+
FGC5658 - Ancestral = T, Derived = C - Results reported above show T- does this equate to Ancestral T, FGC5628-

This means that FGC498 is not a new ISOGG branch under L226 - just another private YSNP of mine. This is more
consistent with additional testing of FGC5628 in the surname cluster that tested FGC5628 negative which is
inconsistent with the above test being FGC498 positive.

Also, this also means FGC5658 is yet another private YSNP of my test. And FGC5618 and FGC5626 remain
equivalents of L226 (or possibly earlier than L226).

Hopefully, Thomas or Astrid will eventually answer my email. There really should be a small web site at
YSEQ that explains this unusual terminology. I wish they would use the standard methodology to avoid
this confusion.

JRW
10-02-2014, 02:23 PM
Robert,

YSEQ provides the sample's allele for the tested base position and whether that allele is derived or ancestral. So, a "C+" means that the sample has the base Cytosine at the tested position and for the sample it is derived. In order to go to the step of "does this equate to..." you will have to use another database such as Ybrowser or cross-reference to NGS test results. One can not infer what the ancestral allele would be from a derived result or what a derived allele would be from an ancestral result just by looking at one's YSEQ results alone.

Hope this helps.

George Chandler
10-02-2014, 02:49 PM
Hi Robert,
It means (as JRW mentioned) that you're positive for FGC5618 & FGC5626 but negative for the other two. Usually a FGC labeled SNP is a newly discovered SNP by them which has not been previously identified. You may want to confirm there is no other name for them (SNP's) created by another sequencing company or provider.

George

RobertCasey
10-04-2014, 12:06 AM
Robert,

YSEQ provides the sample's allele for the tested base position and whether that allele is derived or ancestral. So, a "C+" means that the sample has the base Cytosine at the tested position and for the sample it is derived. In order to go to the step of "does this equate to..." you will have to use another database such as Ybrowser or cross-reference to NGS test results. One can not infer what the ancestral allele would be from a derived result or what a derived allele would be from an ancestral result just by looking at one's YSEQ results alone.

Hope this helps.

The ancestral and derived values are from the YSEQ description of each YSNP - so this is their interpretation. These are not found in the ISOGG version which Thomas also maintains.

According to Greg M, FGC498 has two mutations in the 1K database (but also states that since there are only two independent mutations known in the 1K genomes database) that
would still be a worthy candidate for testing. This YSNP is also part of the Big Y test and all other values are negative (which would make it a private YSNP of mine from my
FGC test). I had these four private YSNPs tested at YSEQ for another L226 Casey submission (who has GD=10 from me) to see if I would luck out an interesting result.

There test results were report as G-

The question is:

Does this mean they found the value of G (and it was a negative result) - this would consistent with other testing.
They tested and found negative for G (they found A) - my original interpretation and would create a new branch - but subsequent testing is inconsistent.

RobertCasey
10-04-2014, 12:14 AM
Hi Robert,
It means (as JRW mentioned) that you're positive for FGC5618 & FGC5626 but negative for the other two. Usually a FGC labeled SNP is a newly discovered SNP by them which has not been previously identified. You may want to confirm there is no other name for them (SNP's) created by another sequencing company or provider.

George

The ISOGG Y chromosome browser (maintained by Thomas K) has no names for this YChr position. The YSEQ lookup of these YSNPs the source that confirms the names (but I submitted these names to them). FGC created these names as part of the interpretation of my FGC YChr test. FGC498 is part of the Big Y test but has no name from FTDNA. Do you have other sources where one can enter a YChr position and see what names have been assigned to the position ?

So it appears that my original interpretation not correct and the italicized version is now verified by you and Greg (hoxgi). I really seems that YSEQ should have a small web site explaining how to interpret their non-standard format.

George Chandler
10-04-2014, 02:54 AM
The ISOGG Y chromosome browser (maintained by Thomas K) has no names for this YChr position. The YSEQ lookup of these YSNPs the source that confirms the names (but I submitted these names to them). FGC created these names as part of the interpretation of my FGC YChr test. FGC498 is part of the Big Y test but has no name from FTDNA. Do you have other sources where one can enter a YChr position and see what names have been assigned to the position ?

So it appears that my original interpretation not correct and the italicized version is now verified by you and Greg (hoxgi). I really seems that YSEQ should have a small web site explaining how to interpret their non-standard format.

Hi Robert,
If you use the Y Browser it does show the name and coding region for bothFGC5618 & FGC5626. If I understand you correct you want to enter the coding region and then look to see what the name is correct? I'm not sure if it's the correct way to reverse search the SNP but if you enter the coding region in the preferences tab where it says "highlight regions" then click on the "update appearance" then click on the custom tracks and click back to the preferences tab you will see the name listed in the highlight features box with the SNP named @yellow. If you are looking to find the coding region just click the browser option then enter the SNP name in the landmark or region box and that will give you the coding region.

Hope this helps.
George

jraiken
11-25-2015, 02:12 AM
Not sure if I should post here, or not.
I have a haplogroup designation of DF21 at FTDNA. I did the R1b-DF21 panel test from Yseq and received my results today. I desperately need help interpreting what it all means. My allele results are as follows:

3588 A631 ChrY 18177387 18177387 T-
3588 A67 ChrY 6704979 6704979 T+
3588 A7099 ChrY 18177379 18177379 G-
3588 CTS353 ChrY 6704770 6704770 T-
3588 CTS4505 ChrY 15684166 15684166 T-
3588 CTS9144 ChrY 18712140 18712140 A-
3588 DF5 ChrY 18393814 18393814 A-
3588 FGC13605 ChrY 18712024 18712024 A-
3588 FGC17318 ChrY 6704738 6704738 A-
3588 FGC19616 ChrY 18177387 18177387 T-
3588 FGC20434 ChrY 18712200 18712200 A-
3588 FGC21907 ChrY 18177433 18177433 A-
3588 FGC23029 ChrY 15683998 15683998 C-
3588 FGC2358 ChrY 18177589 18177589 C-
3588 FGC29225 ChrY 6704963 6704963 G-
3588 FGC3181 ChrY 6704979 6704979 T+
3588 FGC3188 ChrY 15683936 15683936 C+
3588 FGC3197 ChrY 7952608 7952608 T-
3588 FGC3213 ChrY 26722140 26722140 C+
3588 FGC32443 ChrY 18177550 18177550 A-
3588 L605 ChrY 18393536 18393536 G-
3588 L640 ChrY 18393688 18393688 A-
3588 M10094 ChrY 18711888 18711888 T-
3588 M10838 ChrY 6704927 6704927 G-
3588 M12390 ChrY 19088644 19088644 C-
3588 PF3023 ChrY 18393536 18393536 G-
3588 PF7562 ChrY 7952440 7952440 C-
3588 PF936 ChrY 18711888 18711888 T-
3588 PH148 ChrY 6704962 6704962 C-
3588 PH149 ChrY 6705048 6705048 G-
3588 PH3942 ChrY 18712158 18712158 T-
3588 PH4204 ChrY 19088782 19088782 A-
3588 S191 ChrY 18393814 18393814 A-
3588 S3026 ChrY 6704979 6704979 T+
3588 S3058 ChrY 15683936 15683936 C+
3588 S425 ChrY 18712022 18712022 A-
3588 S5488 ChrY 19088630 19088630 C-
3588 V3435 ChrY 18712158 18712158 T-
3588 Y11277 ChrY 19088630 19088630 C-
3588 Y15522 ChrY 7952402 7952402 C-
3588 Y17306 ChrY 18393820 18393820 G-
3588 Y17944 ChrY 15684140 15684140 A-
3588 Y5526 ChrY 18177442 18177442 C-
3588 Y6673 ChrY 18711897 18711897 A-
3588 Y7388 ChrY 15683998 15683998 C-
3588 Y9399 ChrY 18712200 18712200 A-
3588 YP1385 ChrY 18177550 18177550 A-
3588 YP4000 ChrY 7952658 7952658 A-
3588 Z18000 ChrY 18177433 18177433 A-
3588 Z20246 ChrY 18177442 18177442 C-
3588 Z28353 ChrY 18177269 18177269 G-
3588 Z3004 ChrY 15208574 15208574 C-
3588 Z32849 ChrY 6705074 6705074 G-
3588 Z33418 ChrY 7952689 7952689 G-



I received an email from yseq saying that my final branch is A67*

So, what does all that mean in DNA for dummies terminology?

Thanks,

Jacques Aiken

Huntergatherer1066
11-25-2015, 02:51 AM
Those are interesting results given that you're negative for the many downstream branches of A67. Here is the DF21 tree at the Big Tree: http://www.ytree.net/DisplayTree.php?blockID=6 and here is the A67/Little Scottish Cluster portion of the DF21 tree: http://www.ytree.net/DisplayTree.php?blockID=40&star=false It looks like there is just the one A67* NGS sample submitted there right now.

boab007
11-21-2017, 07:10 PM
I realise this is an old thread, but I have had the same result from yseq today. I just wondered what is your 'paper trail' ancestry? Do you have any Scottish ancestry?