PDA

View Full Version : L21 Full Genomes Corp tracking and results



Mikewww
10-04-2013, 01:06 PM
Mark J posted this list for us. I'll repost it here. If you see anyone missing, please report it.

f148325 DF13** MJost z1130-A1-A,
f186947DF13* Edgecombe z9914-E,
fN55408 DF13** Smith z141121,
f11143 DF13 Chandler z9919-A
f28714 DF21/L658 Cain
f20437 DF21/L627 Reynolds
f196041 DF21/S190 Williamson
fN3362 DF21 (21-5909-A, L1336-) Maher
fN36510 DF21 (P314.2-, Z246-) Charles Fueston
f176148 DF41* Duffy
f240201 DF41* Walker
????? DF41 Name with-held (41-1426C-A Variety)
f8999 DF49/M222 Wilson
f159309 DF49/Z2961* (M222-) Trainor
fN7406 DF49/DF23/Z2961/M222 Donaldson
f129036 DF49* Bill Harrison
f117117 DF49* Jay Holladay
f258447 L1335/L1065* Taylor
f107327 L1335/L1065 Iles
f139697 Z251+ Munn (Geno2 tested),
f193834 Z251/L583 Yurzditsky
f77349 Z253/L226 Casey
f233265 Z253/Z2534* Mathieu LE GALL - Brittany, Bretagne
f205635 Z253+ (Z2534-, L1308-, F4036-) Murta
f228772 L513** Reid

http://groups.yahoo.com/neo/groups/R1b-L21-Project/conversations/topics/16091

Celtarion
10-05-2013, 10:51 AM
Hi Mike,

I think that it would be interesting to mention the batch number for every kits ordered so then we know more or less where we are as I don't expect to get the results before mid-december, early january the latest I'd say.

I'm kit 233265 - Batch 5.

Thanks,

Joss.

Dubhthach
10-05-2013, 12:50 PM
f176148 DF41* Duffy - Batch 5

-Paul
(DF41+)

kenmunn
10-05-2013, 02:05 PM
f139697 - batch 5

Williamson
10-05-2013, 03:36 PM
f196041 - batch 4

seferhabahir
10-05-2013, 08:09 PM
f193834 - batch 5

Mikewww
10-06-2013, 01:49 AM
Erik M posted this update to day. I haven't tried to compare this with the earlier posts on this thread:

R1b-P312>L21, 148326, ?, MJost, ?, DF13**, ?, ?
R1b-P312>L21, 186947, ?, Edgecombe, ?, DF13*, ?, ?
R1b-P312>L21, N55408, ?, Smith, ?, DF13*, ?, ?
R1b-P312>L21, 11143, ?, Chandler, ?, DF13* (9919 cluster), ?, ?

R1b-P312>L21, 129036, ?, Bill Harrison, ?, DF49 (DF23-), ?, ?
R1b-P312>L21, 117117, ?, Holladay, ?, DF49 (DF23-), ?, ?
R1b-P312>L21, 159039, ?, Trainor, ?, DF49>DF23>Z2961* (M222-), ?, ?
R1b-P312>L21, 8999, ?, David Wilson, ?, DF49>M222, ?, ?
R1b-P312>L21, N7406, ?, Donaldson, ?, DF49>M222, ?, ?
R1b-P312>L21, ?, ?, ?, ?, DF49>M222, ?, ?

R1b-P312>L21, 228772, ?, Reid, ?, L513**, ?, ?

R1b-P312>L21, 77349, ?, Robert Casey, ?, Z253>L226, ?, ?
R1b-P312>L21, 233265, ?, Mathieu Le Gall, Brittany Bretagne, Z253>Z2534*, ?, ?
R1b-P312>L21, 205635, ?, Murta, ?, Z253 (Z2534-), ?, ?

R1b-P312>L21, 107327, ?, Iles, ?, L1335>L1065, ?, ?
R1b-P312>L21, 258447, ?, Taylor, ?, L1335>L1065*, ?, ?

R1b-P312>L21, N36510, ?, Charles Fueston, ?, DF21 (P314.2- Z246-), phase 5, N
R1b-P312>L21, 20437, ?, David Reynolds, ?, DF21>L627, ?, ?
R1b-P312>L21, 28714, ?, Rory Cain, ?, DF21>L658, ?, ?
R1b-P312>L21, 196041, ?, Alex Williamson, ?, DF21>S190, ?, ?
R1b-P312>L21, N3362, 11R9D, Erik Maher, John Maher b circa 1831 Noughaval Co. Clare, DF21* (L1336 no-call), phase 5, N

R1b-P312>L21, 240201, ?, Walker, ?, DF41 (CTS2501), ?, ?
R1b-P312>L21, 176148, ?, Duffy, ?, DF41, ?, ?
R1b-P312>L21, ?, ?, ?, ?, DF41 (41-1426C-A), ?, ?

R1b-P312>L21, 139697, ?, Munn (Godwin?), ?, Z251, ?, ?
R1b-P312>L21, 193834, ?, Yurzditsky, ?, Z251>L583, ?, ?

Mikewww
11-01-2013, 01:00 PM
Richard Rocca asked this question. I think we have a couple of people who have ordered the fully Y sequencing test from Full Genomes. Please sign in and let us know what is happening. Is David Reynolds engaged in this? I hope we are working him to the wit's end.

I want to make sure to incorporate the results that are relevant into the big haplotypes spreadsheet as well as ensure David has everyone's data so he can do the phylogenetic tree comparisons. Please note that although I have privacy concerns on some things, that does mean I'm not supporting of full Y chromosome sequencing. This is the future.

I've said this before and I think David is thinking about it, but we need to somehow have a format for relevant (to the subclade) results to be shared in a data structured format, like a spreadsheet or a database. This would allow me to easily update into the big haplotypes spreadsheet as new results come in. That spreadsheet can automatically derive haplogroup labels based on phylogenetic tree programming

George Chandler
11-01-2013, 02:51 PM
Has anyone heard from David R lately? I sent him an email some time ago but didn't heard back (as of last night anyway). Some new Geno 2.0 results under L21 were sent to him as well but the spread sheet hasn't been updated yet so I'm guessing he's either really busy or travelling again.

George

Mikewww
11-01-2013, 03:17 PM
Here is one.

f196041 Williamson R1b-P312>L21>DF13>DF21 21-5909-LS

What's interesting on this one is that it is what I call 21-5909-LS or the "Little Scots Cluster." BritainsDNA had already identified two proprietary (I guess) SNPs, S424 and S190 that seem to be found in this variety. Maybe now we'll have the actual physical locations indentified. These can probably be triangulated by having an second probable S190+ test to go along with a known S424+ S190- person.

Cool stuff!



I received my FullGenomes results this afternoon, and I've just had a chance to start looking at them. It's quite a bit of data.

Similar to David Reynolds, FullGenomes is reporting 292 "private" non-INDEL SNPs. These 292 SNPs come in 4 different levels of quality from 0 to 3 stars (*), with *** being the least reliable. The breakdown of my 292 SNPs is as follows:



Quality
Likely Genuine?
Count


no *s
over 99%
10


*
over 95%
13


**
about 40%
55


***
about 10%
214



FullGenomes considers those with 0* or 1* as high quality, and reports that they have found 23 high quality private SNPs in my Y-DNA. These new SNPs were named FG1549 to FG1571. (I foresee a lot of FG SNPs in the future.)

If I understand my results correctly, there is a gentleman, NA12043 tested in the past, who looks to have a number of the Little Scottish Cluster SNPs as I have. I think these shared SNPs reduce the number of novel SNPs from my DNA. So, where David had about 40 new high quality SNPs, I have only 23.

In terms of INDELs, they found 32 private INDELs of which 2 were high quality.

The high quality private SNPs are the following:


SNPhg19ancder
FG15493779037AC
FG15503899172GT
FG15514511965AG
FG15524687827AG
FG15536067820AT
FG15547952608TC
FG15557992480CT
FG15568790228AG
FG15578980644TA
FG15589085250GT
FG15599114725GT
FG156013128633AC
FG156113979797TC
FG156215117619GT
FG156315452508GA
FG156417112718TA
FG156517546935CG
FG156618017942GA
FG156721475911GA
FG156821617233AC
FG156923275266CG
FG157026722140AC
FG157128675156TC


I recognize some of my shared and private SNPs as the ScotlandsDNA SNPs, but I still have to figure that out.

Regards,
Alex
kit 196041
FG P9UH4 http://www.anthrogenica.com/showthread.php?170-DF21-(L21-gt-DF13-gt-DF21)-and-Subclades-(DF5-S191-P314-2-S190-etc)&p=17121&viewfull=1#post17121

Mikewww
11-01-2013, 03:24 PM
Here is another, from our illustrious leader no less. George, I'm pretty sure he is just really busy. I certainly hope that's it. I've heard rumors of various projects he is working on. They are just rumors but that would account for a lot of extra activity for him.

f20437 Reynolds R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>CTS3655>L627>L626+ 3c1.3g 21-246-255-3655-627


I got my results from Full Genomes; SNP calls were consistent with my previous tests. For non-INDels, 292 "private" SNPs were found, of which 40 were high quality (95+% chance of being valid calls), and were named FG575 to FG614. 31 "private" INDels were found, of which one was high quality (ChrY:23127168, T->TA).

No SNPs were found that might be equivalent to DF21 or CTS3655. Three high quality mutations were found that are present in my results, as well as the results of public datasets HG00116, HG00242, and PGP104. These three SNPs are located somewhere between CTS3655 and Z246 and may well be equivalent to existing SNPs.
5185401 G->A
9129841 T->G
8381834 C->G

I am not shown as derived for either L1446 or L1447, but until I get my BAM file, I will not know for certain that they are ancestral (vs no-calls).

Next big step will be when Rory gets his results and we are able to compare which we might have in common.

Regards,
david


"Private" high quality SNPs


SNP
hg19
anc
der


FG575
2965010
C
G


FG576
3025790
C
T


FG577
3775282
G
T


FG578
4124386
T
G


FG579
6328811
A
C


FG580
7059475
C
T


FG581
7373407
C
G


FG582
8039775
T
C


FG583
8067756
C
G


FG584
8341127
A
T


FG585
8394820
T
C


FG586
9101362
G
A


FG587
13801643
C
T


FG588
13941880
A
G


FG589
14011877
G
T


FG590
14115486
A
G


FG591
14202036
C
T


FG592
14708498
C
T


FG593
14961679
T
C


FG594
15051218
C
T


FG595
15750967
T
A


FG596
16357166
G
A


FG597
16469744
T
C


FG598
16609044
C
A


FG599
17622242
G
A


FG600
17942236
G
C


FG601
18408759
A
G


FG602
19108196
C
T


FG603
21456130
C
T


FG604
21470722
G
T


FG605
21762362
C
G


FG606
22471533
C
A


FG607
22771173
T
C


FG608
22834676
T
A


FG609
23342920
G
A


FG610
23458488
G
T


FG611
24932695
C
T


FG612
26203308
C
T


FG613
27647624
G
C


FG614
28579952
A
T

http://www.anthrogenica.com/showthread.php?170-DF21-(L21-gt-DF13-gt-DF21)-and-Subclades-(DF5-S191-P314-2-S190-etc)&p=16622&viewfull=1#post16622

Mikewww
11-01-2013, 03:35 PM
This is not the complete list, but I'll get it started

f20437 Reynolds R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>CTS3655>L627>L626 + 3c1.3g 21-246-255-3655-627 (in)
f196041 Williamson R1b-P312>L21>DF13>DF21 21-5909-LS (in)
f28714 Cain R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>L658+ 21-246-255-658
f148326 Jost R1b-P312>L21>DF13**
f240201 Walker R1b-P312>L21>DF13>DF41** 41-1426C
f176148 Duffy R1b-P312>L21>DF13>DF41** 41-1013
f77349 Casey R1b-P312>L21>DF13>Z253>Z2534>L226+ 253-2534-226-C1
f159039 Trainor R1b-P312>L21>DF13>DF49>DF23>Z2961* 49-2329-11-HyM
f8999 Wilson R1b-P312>L21>DF13>DF49>DF23>Z2961>M222 49-2329222-55717
f228772 Reid R1b-P312>L21>DF13>L513* 513- uas

The L513+ guy posted he ordered but I haven't seen him on any other lists.

I would think this guy would be on the list too.
f16646 Conroy R1b-P312>L21>DF13>DF49>DF23>Z2961>M222>PF1169+ 49-2329222-48714-A

Can anyone verify either f228772 or f16646? [[ update: Reid confirmed he has ordered ]]

Also should have one from this subgroup but trying to locate the kit #.
? Mcguire R1b-P312>L21>DF13>L513 L69.5+ 513-A2-M

Dubhthach
11-01-2013, 04:14 PM
I also have it on order:
176148 - Duffy - DF41**

It should be interesting to see what myself and Larry share (or don't share).

-Paul
(DF41+)

Mikewww
11-01-2013, 04:49 PM
This is not the complete list, but I'll get it started
...
I would think this guy would be on the list too.
f16646 Conroy R1b-P312>L21>DF13>DF49>DF23>Z2961>M222>PF1169+ 49-2329222-48714-A

Can anyone verify .... f16646?

f20437 Reynolds R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>CTS3655>L627>L626 + 3c1.3g 21-246-255-3655-627 (in)
f196041 Williamson R1b-P312>L21>DF13>DF21 21-5909-LS (in)
f28714 Cain R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>L658+ 21-246-255-658
f148326 Jost R1b-P312>L21>DF13**
f240201 Walker R1b-P312>L21>DF13>DF41** 41-1426C
f176148 Duffy R1b-P312>L21>DF13>DF41** 41-1013
f77349 Casey R1b-P312>L21>DF13>Z253>Z2534>L226+ 253-2534-226-C1
f159039 Trainor R1b-P312>L21>DF13>DF49>DF23>Z2961* 49-2329-11-HyM
f8999 Wilson R1b-P312>L21>DF13>DF49>DF23>Z2961>M222 49-2329222-55717
f228772 Reid R1b-P312>L21>DF13>L513* 513- uas (batch 5)
f226869 Maguire R1b-P312>L21>DF13>L513 L69.5+ 513-A2-M (batch 5)


There must be an L1335+ L1065+ Scots guy in this.

Mag Uidhir 6
11-01-2013, 05:02 PM
For all (sorry I'm late to the party),
The R-L513-A-2 group within the Airghialla Mag Uidhir Project have a kit in Batch #5 with FGC:

226869 McGuire John Maguire c1816-1871 Co. Galway R1b1a2 R-M269 L513+, L69+

We are fervently hoping for a definitive SNP besides L69.5+ (pesky little thing found in multiple Hg, and is the fifth iteration of L69).

Cheers
Brad

George Chandler
11-01-2013, 05:15 PM
Ok thanks Mike. I kind of figured so but thought I would ask. It will be interesting to see the difference in age estimates that come from the new SNP finds if the 1 per 3 or 4 generations holds up. I'm trying to get participation from another person to see if it does but haven't had any sucess yet.

Sealgair
11-01-2013, 06:42 PM
Mike,

Two more DF21 guys for the list.

N3362, Maher, R1b-P312>L21>DF13>DF21, 21-5905-A, (Batch 5)
N36510, Fueston, R1b-P312>L21>DF13>DF21, 21-uas, (Batch 5)

MJost
11-01-2013, 06:58 PM
This is the list I have to date. MJost


DF13** MJost (148326) z1130-A1-A,
DF13* Edgecombe, (186947) z9914-E,
DF13** Smith (N55408) z141121,
DF13 Chandler (11143) z9919-A,
DF21/L658 Rory Cain (28714),
DF21/L627 David Reynolds (20437) under analysis,
DF21/S190 Alex Williamson (196041) in analysis,
DF21 Erik Maher, (N3362) (21-5909-A, L1336-),
DF21 (P314.2-, Z246-) Charles Fueston (N36510) Batch 5,
DF41* Duffy (176148) Batch 5,
DF41* Walker (240201),
DF41 Name with-held (41-1426C-A Variety),
DF49/M222 David Wilson (8999),
DF49/Z2961* (M222-) Trainor (159309),
DF49/DF23/Z2961/M222 Ron Donaldson (N7406),
DF49* Bill Harrison (129036),
DF49* Jay Holladay (117117),
L1335/L1065* Taylor (258447),
L1335/L1065 Iles, (107327),
Z251+ Munn (139697) (Geno2 tested) batch 5,
Z251/L583 Yurzditsky, (193834),
Z253/L226 Robert Casey (77349),
Z253/Z2534* Mathieu LE GALL - Brittany, Bretagne (233265) Batch 5,
Z253+ Murta (205635) (Z2534-, L1308-, F4036-),
L513** Reid (228772),
L555 Irvine -(22874) Batch 5

seferhabahir
11-02-2013, 03:28 AM
This new thread needs to be merged in with the already existing "L21 Full Genome tracking and results" thread (or else vice versa) so I know what thread to post in...

http://www.anthrogenica.com/showthread.php?1402-L21-Full-Genome-tracking-and-results

[[[ Mikewww/Moderator on 02Nov2013: This is a bit weird. I couldn't find that other thread except through your link. I merged everything together so it should okay now. ]]]

Irvine
11-02-2013, 12:08 PM
Irvine - FtDNA (22874) - R1B>L21>DF13>Z251>L555 has ordered full Y test - Batch 5

MJost
11-02-2013, 12:58 PM
Irvine - FtDNA (22874) - R1B>L21>DF13>Z251>L555 has ordered full Y test - Batch 5
Thanks for the update!

MJost

Mikewww
11-02-2013, 06:57 PM
I found some transposed digits and I can only usefully apply this stuff if I put it in a structured format so I added a column internally into the R1b-L21 haplotypes spreadsheet. First pass, below is what I have. As soon as I/we can figure out which of all the novel FGC SNPs are likely public I'll incorporate them into the spreadsheet AND "(FG)" will appear in the Revelant/downstream SNPs column, like "(G2)" now appears and "(C2)" soon will.


f11143 Chandler England FG R1b-P312>L21>DF13 z9919-A
fN55408 Smith zzCountry FG R1b-P312>L21>DF13* z141121
f148326 zzzUnk(Ross) zzCountry FG R1b-P312>L21>DF13* z1130-A1-A
f186947 Edgcombe England FG R1b-P312>L21>DF13* z9914-E
fN36510 Fueston zzCountry FG5 R1b-P312>L21>DF13>DF21 21- uas
fN3362 Maher Ireland C2/FG R1b-P312>L21>DF13>DF21 21-5909-A
f196041 Williamson Scotland C2/FGd R1b-P312>L21>DF13>DF21 21-5909-LS
f20437 Reynolds zzCountry C2/FGd R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>CTS3655>L627>L626+ 21-246-255-3655-627
f28714 Cain Ireland FG R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>L658+ 21-246-255-658
f176148 Duffy Ireland FG5 R1b-P312>L21>DF13>DF41** 41-1013
f240201 Walker Scotland FG R1b-P312>L21>DF13>DF41** 41-1426C
f129036 Harrison England FG R1b-P312>L21>DF13>DF49* 49*-2526-B
f117117 Holladay England FG R1b-P312>L21>DF13>DF49* 49*-1014
fN7406 Donaldson Ireland FG R1b-P312>L21>DF13>DF49>DF23>Z2961>M222 49-2329222- uas
f8999 Wilson Ireland C2/FG R1b-P312>L21>DF13>DF49>DF23>Z2961>M222 49-2329222-55717
f107327 Iles England FG R1b-P312>L21>DF13>L1335>L1065** 1335-Sc-2415
f258447 Taylor zzCountry FG R1b-P312>L21>DF13>L1335>L1065** 1335-Sc-2437
f228772 Reid Ireland FG6 R1b-P312>L21>DF13>L513 513- uas
f226869 McGuire Ireland FG5 R1b-P312>L21>DF13>L513>L69.5 513-A2-M
f139697 Godwin zzCountry FG5 R1b-P312>L21>DF13>Z251 251-1124-9
f205635 Murta Ireland FG R1b-P312>L21>DF13>Z253 253-1716-11
f233265 Le Gall France C2/FG5 R1b-P312>L21>DF13>Z253>Z2534 253-2534- uas
f77349 Casey(SCarolina) Ireland FG R1b-P312>L21>DF13>Z253>Z2534>L226+ 253-2534-226-C1

irishreid33
11-03-2013, 01:23 AM
Mike,
My Batch at UCLA is 6 and its expected to be six weeks more

Michael Reid f228772
Full Genome : 7WDDR

irishreid33
11-03-2013, 01:27 AM
Michael Reid Batch 6
F228762
Full genome kit 7WDDR

irishreid33
11-03-2013, 01:28 AM
Correction f228772 for Reid

David Wilson
11-03-2013, 05:21 PM
Mike, I am also batch 6 (UCLA) at FG. I don't have any recent projections for results, but didn't expect to hear anything before late November at the earliest and perhaps not until January.

David Wilson f8999

George Chandler
11-03-2013, 10:43 PM
Has there been anything interesting from these tests results regarding the new extra STR's?

Rory Cain
11-04-2013, 08:49 PM
Has there been anything interesting from these tests results regarding the new extra STR's?

Hmm, well following the first DF21 result, one might reasonably expect that when processing the 2nd DF21, Fullgenomes would compare the two. After all, both are in the Fullgenomes database. Then we could answers questions like yours, above.

For whatever reason though, that analysis did not occur. A short-cut to compensate for the massive blow-out in delivery times?

Fortunately we have a work around, as the two guys concerned are subject matter experts and will likely develop their own spreadsheets to capture which new SNPs have a wider application.

George Chandler
11-05-2013, 12:30 AM
On the other thread Justin mentioned they are working on getting something similar to YFull in place. It will be really interesting to see a comparison of the new markers. I'm guessing Mike may add another tab to his L21 spreadsheet as he did with the 111 marker results (but I don't want to speak for him).

George

Mikewww
11-05-2013, 12:52 AM
On the other thread Justin mentioned they are working on getting something similar to YFull in place. It will be really interesting to see a comparison of the new markers. I'm guessing Mike may add another tab to his L21 spreadsheet as he did with the 111 marker results (but I don't want to speak for him).

George

I'm kind of waiting to see what David Reynolds comes up with. I don't think we'd want to add all of the SNPs for every individual into the spreadsheet as that would blow it up immediately.

What's important to each haplogroup project are the relevant SNPs. I've proposed a format for configuring relevant SNP master records by subclade... probably one master record for each DF63, L21**, DF41, DF49xM222, M222, L513/DF1, DF21, Z253, Z255, Z251, CTS4466, L371, etc.

From the master records I could derive from raw results files a row or string of relevant SNPs that I could easily add into my spreadsheets. We'd have a "no typing", "no eye", "no thinking" dependent method for consolidating relevant SNPs into

Of course the master records would have to be manually typed with detailed knowledge of the phylogenetic tree and the corresponding kit #s/yseach ID's typed in during the extraction process, but we could let formulas pick out the appropriate SNPs.

David Reynolds is aware of my line of thought and had probably already considered that anyway. He's been heads down on something so we'll see. As a backup, although this would be Chromo 2 only (Geno 2 is already done with the YDNA SNP report screen), I will receive a list of downstream SNPs from L21 so I could use that to incorporate Chromo 2 results more comprehensively/accurately.

I haven't talked to David for a while. For all I know he has something to do with Yfull.

I haven't really looked at YFull. I've always said we need a "Ysearch for SNPs". Perhaps that is what it is.

George Chandler
11-05-2013, 03:25 AM
I haven't talked to David for a while. For all I know he has something to do with Yfull.

I haven't really looked at YFull. I've always said we need a "Ysearch for SNPs". Perhaps that is what it is.

It's a service you pay to have your FGS results analyzed and displayed which is based out of Russia. There is a R1a project started on it which displays all the the new STR's. I was wondering if you were going to make another tab on your spreadsheet to include those new markers under L21. It displays many of the STR's we already have and more (as I'm sure you're already aware). It will be interesting to see what David R comes up with in terms of a SNP comparison spreadsheet.

Mikewww
11-05-2013, 05:57 AM
... I was wondering if you were going to make another tab on your spreadsheet to include those new markers under L21. It displays many of the STR's we already have and more (as I'm sure you're already aware). ...

Right now I have no plans to go beyond the 111 Y STRs. I think we need to build that up a bit more before adding more STRs. All of this is only valuable if you a lot to compare with. The size of the matching database is important.

I also need an easy way to import the STRs from whatever format they are in. Right now I have an import/transform spreadsheets (automation) that can take any current FTDNA project Y classic screen or any Ysearch query report and merge them into the standard format, which is the old FTDNA Y STR report screen with 389ii-i instead of 389-2.

MacUalraig
11-05-2013, 07:06 AM
Hmm, well following the first DF21 result, one might reasonably expect that when processing the 2nd DF21, Fullgenomes would compare the two. After all, both are in the Fullgenomes database. Then we could answers questions like yours, above.

For whatever reason though, that analysis did not occur. A short-cut to compensate for the massive blow-out in delivery times?

Fortunately we have a work around, as the two guys concerned are subject matter experts and will likely develop their own spreadsheets to capture which new SNPs have a wider application.

Rory, the impression I was under is that the customer to customer comparisons are being left to the customers themselves due to the privacy angle (although they could have a flag or tick box somewhere to deal with that I guess). At the moment most people probably know who the other testers in their neighbourhood are anyway so I don't see it as a big issue.

MacUalraig

Dubhthach
11-05-2013, 11:41 AM
Given the tsunami of data we are going to be presented with we really need to look into building a custom MySQL database (or the like). At least then you could separate relevant data out into separate Tables/Views. Any DBA's (Database Admin's) out there in the wider community? Unfortunately I've never really spent much time looking at actual Database structure (just managing the underlying systems)

-Paul
(DF41+)

Mikewww
11-05-2013, 02:58 PM
Given the tsunami of data we are going to be presented with we really need to look into building a custom MySQL database (or the like). At least then you could separate relevant data out into separate Tables/Views. Any DBA's (Database Admin's) out there in the wider community? Unfortunately I've never really spent much time looking at actual Database structure (just managing the underlying systems)

-Paul
(DF41+)
At about that time you end up having a server and start bringing in some other operational and security requirements. I won't go into that kind of thing for a hobby. That's a job, but I see there are Russians who might, or might have already.

RobertCasey
11-05-2013, 03:37 PM
I have a fairly operational MySQL database - but it is only based on FTDNA YSTR and YSNP reports. I manually add David Reynold's data into my exported spreadsheets. He adds YSNPs for WTY (initial goal) and then expanded to Nat Geo 2.0 tests. The CROMO2 and Full Genomes are the next obvious steps and these are really going to tax us. Plus David R, Mike W and myself are primarily L21 researchers - even though Mike W tracks L21 cousins as well. I am sure David Reynolds is a little distracted with trying to understand his Full Genomes results and how to share/compare them with the genetic community. My Full Genomes test (L226+) is in Batch 4 and is due in "early" November. Once I receive these files, I will look into how to import the YSNPs and YSTRs into my MySQL database. I have a recent volunteer to assist me with getting the MySQL database more operational (working on automating updates). For every new submission at 67 markers, you have to manually parse the Surname and Origin fields which is very time consuming for 26,000 submissions. My MySQL skills are not the strongest - but I do have strong database design skills and understand what is needed. I was hoping to have a more operational database before "tsunami" arrived, but I think our volunteer community is going to be stretched for near term. I do have 26,000 67 marker submissions that are L21 candidates (but include many L21 cousins to date). I agree that if anyone has MySQL (and php) skills, now is the time to pitch in and help the existing volunteer community with more advanced tools and databases that are required. As Mike W mentioned in previous posts, proposing some standards for output reports would get more consistency in our methodologies.

For instance, tracking individual 20,000 plus YSNPs properly produces the need for a YSNP table with 100,000 plus columns which databases are not well suited for. We need to normalize tables (break up the tables) into more reasonable amounts. Even tracking the mere 150 YSNPs under L21 makes a very large table, this becoming a problem (do we really need to load several thousand M222 negative test results for L513 and other non-DF49 submissions - which I did for a while). With significant convergence between L21, U106, U152 and DF27, many submissions with no known signatures may have to be put into multiple tables. There is also significant convergence between DF13 sons as well. David Reynolds already has started to normalize his tables under L21 - breaking them up into the large DF13 sons and others. This saves time and space of having to load L513 YSNPs into DF21 tables and makes the tables more user friendly to consume as well. Also, Full Genomes has stated that they will eventually produce their own database as well - but we still have to merge this potentially new database with FTDNA YSNP reports, WTY reports, Nat Geo raw data and Britain's DNA raw data - not an easy task. Unfortunately, a good programmer for one year is more money than all the revenue of Full Genomes to date (hopefully FG will grow fast as others have).

Rory Cain
11-05-2013, 08:47 PM
Rory, the impression I was under is that the customer to customer comparisons are being left to the customers themselves due to the privacy angle (although they could have a flag or tick box somewhere to deal with that I guess). At the moment most people probably know who the other testers in their neighbourhood are anyway so I don't see it as a big issue.

MacUalraig

Oh dear, dropping their pants and bending over for the privacy freaks, who want to see everyone else's results but hide theirs. Has anyone ever known a privacy freak to give anything to the wider DNA community the way guys like David reynolds, Robert Casey, Mike W et. a.l do? On the contrary, look at the privacy freak who allowed Walk the Y to find L130 for him, but then treated it like his own property. He locked it away for himself until other companies started testing for it years later and found more L130s. I had suspected L130 might be under DF21 and contacted that "proprietor" of L130 numerous times, without even the basic courtesy of a reply. So from where I stand that guy hasn't created a positive image of privacy freaks.

Family Tree DNA learnt from that lesson the the next Walk The Y sale was held on the basis that all new SNPs found would be treated as public. Sure the privacy freaks can still have their standard Y12 etc tests kept private. But out there at the cutting edge, as we have seen from private "ownership" of L130, "breaking news" needs to be got out to researchers with intellect and community service ethos. I don't believe the privacy freaks qualify under either of those criteria.

This bending to privacy freaks raises a cloud over recruiting further testees into Fullgenomes, as the recruiter may not receive much reward for their efforts if the test recruit opts for privacy. I would certainly be cautious about paying for a test for someone else, as I have done in the past and as I know others also do.

Thanks for providing an answer, MacUairaig. You made an honest attempt. However given that my Fullgenomes account provides a "share" button and I can see from my account that the two guys I referred to have both clicked "share" with each other and with me, I am not sure your answer was right, or whether indeed it was a short-cut in the interpretation service to compensate for taking seven months with the raw data?

RobertCasey
11-05-2013, 10:50 PM
Irvine - FtDNA (22874) - R1B>L21>DF13>Z251>L555 has ordered full Y test - Batch 5

One of my favorite surname projects - look forward to looking at this data. The Irvine project is probably the best covered surname with 67 and 111 markers and will greatly benefit from private YSNPs to understand how the current groupings evolved over time. L555 et al were just a little too old to do the trick. My only concern is getting a source for testing these private YSNPs. If Full Genomes or FTDNA does not make individual or groups of YSNPs available for testing for private YSNPs, your test and my L226 FG test will not provide much help for our genealogical research. I may help break up Z253/Z2534 and you may help break up Z251 - but that does not solve our genealogical brick walls.

RobertCasey
11-05-2013, 11:16 PM
This bending to privacy freaks raises a cloud over recruiting further testees into Fullgenomes, as the recruiter may not receive much reward for their efforts if the test recruit opts for privacy. I would certainly be cautious about paying for a test for someone else, as I have done in the past and as I know others also do.


I continue to have concerns about the database support that Full Genomes will provide. At times, they state they will provide a common database for analysis. At other times, I see statements implying we already have enough support via downloads. If they depend on Mike W, David R and myself for database support - their business model will be challenged as we have jobs already and could barely keep up before the tsunami of information that has already begun to hit.

Privacy makes little sense for YSNP research like the Full Genomes test. They need to make all testers submit their submission for public view - to protect themselves and allow the few who want to do their private research to do their research. But keeping Full Genomes tests private is pretty silly as nobody will know your results and can help them analyze their data. You can only make progress if we can compare our results to know what to test next and how the YSNPs are related. Privacy is a good excuse to not develop a good database. However, we should expect to pay for this database and creating it and maintaining it is probably not included in their testing costs today. Eventually, IT costs will far exceed testing costs, so the failed 23andme maintenance model will have to be brought back some day (they were just a little too early adopter).

Mikewww
11-06-2013, 12:10 AM
... For instance, tracking individual 20,000 plus YSNPs properly produces the need for a YSNP table with 100,000 plus columns which databases are not well suited for. We need to normalize tables (break up the tables) into more reasonable amounts. Even tracking the mere 150 YSNPs under L21 makes a very large table, this becoming a problem (do we really need to load several thousand M222 negative test results for L513 and other non-DF49 submissions - which I did for a while). With significant convergence between L21, U106, U152 and DF27, many submissions with no known signatures may have to be put into multiple tables. There is also significant convergence between DF13 sons as well. David Reynolds already has started to normalize his tables under L21 - breaking them up into the large DF13 sons and others. This saves time and space of having to load L513 YSNPs into DF21 tables and makes the tables more user friendly to consume as well.
You've hit the nail on the head. There are different tasks involved. One is the build out of the public Y phylogenetic tree of mankind. That's a huge task in itself. I think the scientists/formal research organizations might need to lead that effort.

Another task set is the series of parallel tasks down at the "last 1500 year" level. That's what will be most interesting to genealogists and historians, in my opinion. It makes no sense to have one gargantuan project for that. Each subclade has to pursue that according to their own depth of interest, financing and technical cabilities. However, I hate to see all of us re-inventing data formats and transformation because these things should all be modular building blocks.


.. Also, Full Genomes has stated that they will eventually produce their own database as well - but we still have to merge this potentially new database with FTDNA YSNP reports, WTY reports, Nat Geo raw data and Britain's DNA raw data - not an easy task. Unfortunately, a good programmer for one year is more money than all the revenue of Full Genomes to date (hopefully FG will grow fast as others have).

I think it would take a lot of resources to build a large database quickly. When I looked at the publicly available information on FG Corp, I don't know. I know that they have two good folks, at least that I can name. The rest is a little elusive. I think the only approach to move quickly to compete with an FTDNA or BritainsDNA would be to copy the data like one of the Russian web sites does. If copied and used for commercial purposes, I don't think too highly of that. I'm not sure what countries that can or can't be done in.

I used to have a development staff. For these kinds IT projects - for widespread uses - it take many times longer than originally estimated. We used to joke about using a programmer's history and personality when guaging how many times to multiple his/her estimate by. Throwing more (expensive) programmers at the situation can actually slow things down in many situations.

George Chandler
11-06-2013, 04:53 AM
For me the most interesting will be the SNP's discovered everything below L21. It will be interesting to see which of the main SNP's below DF-13 find a common ancestral SNP and which don't.

Dubhthach
11-06-2013, 09:12 AM
I used to have a development staff. For these kinds IT projects - for widespread uses - it take many times longer than originally estimated. We used to joke about using a programmer's history and personality when guaging how many times to multiple his/her estimate by. Throwing more (expensive) programmers at the situation can actually slow things down in many situations.

Awh "Brooks's law" : "adding manpower to a late software project makes it later"

One of the hazards of the software business that's for sure.

Does anyone know with regards to "unique SNP's" identified in a Fullgenome sample do they alter this if for example the same SNP is found in another FullGenome kit? For example we know that both David and Alex had a batch of unique SNP's found in them, if for example Rory (another DF21) get's his results back and he shares some of these unique snp's (with either David or Alex) will it declare that they are present in another FG sample?

-Paul
(DF41+)

Williamson
11-06-2013, 10:00 AM
Does anyone know with regards to "unique SNP's" identified in a Fullgenome sample do they alter this if for example the same SNP is found in another FullGenome kit? For example we know that both David and Alex had a batch of unique SNP's found in them, if for example Rory (another DF21) get's his results back and he shares some of these unique snp's (with either David or Alex) will it declare that they are present in another FG sample?


As of right now, FullGenomes assigns FG-numbers to the SNPs that are high quality private SNPs. I'd guess that if two kits shared any of the new FG series SNPs, then they would indicate that somehow. Certainly I can't imagine they would want to assign multiple FG names to the same SNP.

With regard to the discussion around storing the SNPs in a database, I assume you wouldn't want to create a table with hundreds or thousands of columns. Likely, the best solution would be to store the kit number, the location of the SNP, what the mutated value is, and the quality. That would give you a couple thousand rows or so per customer. You'd have separate tables translating positions to SNP names, etc. INDELs could be handled in a similar way. The STR results would require something different.

Based solely on my own experience so far analyzing the FG results, I think the bigger problem lies in validating the SNPs. Each of the SNPs FG reports has it's own quality. The top quality ones are easy, and I take it are very reliable. The real problem is with the lower quality SNPs. There are 10 times as many low quality SNPs than high quality ones, and some may or may not be real. I have encountered situations were one of my high quality SNPs appears as a lower quality SNP for someone else, who might reasonably be positive for it. Without Sanger sequencing the results, you can't be sure if you share it or not.

Alex
(kit 196041)

Rory Cain
11-06-2013, 08:02 PM
Does anyone know with regards to "unique SNP's" identified in a Fullgenome sample do they alter this if for example the same SNP is found in another FullGenome kit? For example we know that both David and Alex had a batch of unique SNP's found in them, if for example Rory (another DF21) get's his results back and he shares some of these unique snp's (with either David or Alex) will it declare that they are present in another FG sample?

-Paul
(DF41+)
Paul, as I understand it, the answer is "No". After David first received his belated Batch 3 results with 40 new SNPs numbered FG575-FG614, Alex was one of the lucky lottery winners from Batch 4 to receive results. Against David's 40, Alex had only 23 new SNPs. Possibly it would have been more except some already occurred in David's kit, one assumes. I asked Alex the same question you are asking, and Alex advised that Fullgenomes had NOT provided him with an "internal" comparison (i.e. with other Fullgenomes clients), only an external comparison with !K Genomes. Alex indicated he would have to dig to find what SNPs he shared with David. As I share with both, I see that both their status reports read "We have processed your kit and are analyzing the results". In practice, that appears to mean that David and Alex are doing their own analyses.

I had also asked David about his L1446 & L1447 status. He did not know as Fullgenomes had not reported on it. It's something else that David says he will have to dig for himself, when he eventually gets access to his raw data. Apparently that still hasn't happened or he would have upgraded the L1446/ L1447status of the CTS3655 sub-group in his R-DF21 Project. It appears that in addition to the 6-8 weeks delivery time blowing out to more like 6-8 MONTHS, that an incomplete comparison report is provided that still leaves clients waiting for their as-yet undelivered raw data, leaving the client to perform his own comparison, whether or not he is skilled to do so. I hope I am wrong, but that's what I'm hearing.

George Chandler
11-07-2013, 12:47 AM
I found some transposed digits and I can only usefully apply this stuff if I put it in a structured format so I added a column internally into the R1b-L21 haplotypes spreadsheet. First pass, below is what I have. As soon as I/we can figure out which of all the novel FGC SNPs are likely public I'll incorporate them into the spreadsheet AND "(FG)" will appear in the Revelant/downstream SNPs column, like "(G2)" now appears and "(C2)" soon will.


f11143 Chandler England FG R1b-P312>L21>DF13 z9919-A
fN55408 Smith zzCountry FG R1b-P312>L21>DF13* z141121
f148326 zzzUnk(Ross) zzCountry FG R1b-P312>L21>DF13* z1130-A1-A
f186947 Edgcombe England FG R1b-P312>L21>DF13* z9914-E
fN36510 Fueston zzCountry FG5 R1b-P312>L21>DF13>DF21 21- uas
fN3362 Maher Ireland C2/FG R1b-P312>L21>DF13>DF21 21-5909-A
f196041 Williamson Scotland C2/FGd R1b-P312>L21>DF13>DF21 21-5909-LS
f20437 Reynolds zzCountry C2/FGd R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>CTS3655>L627>L626+ 21-246-255-3655-627
f28714 Cain Ireland FG R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>L658+ 21-246-255-658
f176148 Duffy Ireland FG5 R1b-P312>L21>DF13>DF41** 41-1013
f240201 Walker Scotland FG R1b-P312>L21>DF13>DF41** 41-1426C
f129036 Harrison England FG R1b-P312>L21>DF13>DF49* 49*-2526-B
f117117 Holladay England FG R1b-P312>L21>DF13>DF49* 49*-1014
fN7406 Donaldson Ireland FG R1b-P312>L21>DF13>DF49>DF23>Z2961>M222 49-2329222- uas
f8999 Wilson Ireland C2/FG R1b-P312>L21>DF13>DF49>DF23>Z2961>M222 49-2329222-55717
f107327 Iles England FG R1b-P312>L21>DF13>L1335>L1065** 1335-Sc-2415
f258447 Taylor zzCountry FG R1b-P312>L21>DF13>L1335>L1065** 1335-Sc-2437
f228772 Reid Ireland FG6 R1b-P312>L21>DF13>L513 513- uas
f226869 McGuire Ireland FG5 R1b-P312>L21>DF13>L513>L69.5 513-A2-M
f139697 Godwin zzCountry FG5 R1b-P312>L21>DF13>Z251 251-1124-9
f205635 Murta Ireland FG R1b-P312>L21>DF13>Z253 253-1716-11
f233265 Le Gall France C2/FG5 R1b-P312>L21>DF13>Z253>Z2534 253-2534- uas
f77349 Casey(SCarolina) Ireland FG R1b-P312>L21>DF13>Z253>Z2534>L226+ 253-2534-226-C1


You can now add McCeney kit#2224 from the 9919-A5 type to the list for FGS

MJost
11-07-2013, 01:46 AM
You can now add McCeney kit#2224 from the 9919-A5 type to the list for FGS

Gr8! Now that will be a key kit for you to measure against.

MJost

George Chandler
11-07-2013, 02:18 AM
I think so too. The next is to get the 9919A-1 custer tested and we're working on it.

MJost
11-07-2013, 02:35 AM
Even better!

MJost

kmaclea
11-08-2013, 05:09 PM
Just joined over here.

As George said, George and Erik and I have begun raising money to test in the 9919-A1 variety (my own variety). If anyone is interested in contributing, we would be happy to receive additional donations. We currently have $700 contributed.

Kyle (ysearch WZCV3, R-DF13*, 9919-A1)

MJost
11-08-2013, 05:46 PM
My FG profile page now is showing about a 60% complete status!

Kit number: 0FW1R

MJost

MacUalraig
11-08-2013, 06:25 PM
My FG profile page now is showing about a 60% complete status!

Kit number: 0FW1R

MJost

Same here - not sure how literally we should take it!? Batch 4.2 should be in around now...

MacUalraig

MJost
11-08-2013, 06:34 PM
I have to agree with you. The percentage isn't annotated as to which process is engaged or have been completed.

MJost

Mikewww
11-15-2013, 03:25 AM
I've got 27 now. Is this the right folks? How does the analysis work? Can we get a list of SNPs per person downstream of L21?

f8999 Wilson 49-2329222-55717
fN3362 Maher 21-5909-1336
f226869 McGuire 513-A2-M
f228772 Reid 513- uas
f193834 Yurzditsky 251-11EE
f148326 zzzUnk(Ross) z1130-A1-A
f28714 Cain 21-246-255-658
f20437 Reynolds 21-246-255-3655-627
f129036 Harrison 49*-2526-B
f11143 Chandler z9919-A
f2224 McCeney z9919-A5
fN55408 Smith z141121
f186947 Edgcombe z9914-E
f196041 Williamson 21-5909-LS
fN36510 Fueston 21- uas
f240201 Walker 41-1426C
f176148 Duffy 41-1013
f117117 Holladay 49*-1014
f258447 Taylor 1335-1065-Sc2437
f107327 Iles 1335-1065-Sc2415
f77349 Casey(SCarolina) 253-2534-226-C1
f22874 Irvine 251-555-Irw
fN7406 Donaldson 49-2329222- uas
f139697 Godwin 251-1124-9
f205635 Murta 253-1716-11
f233265 Le Gall 253-2534- uas
f273282 Trainor 49-23- uas

MJost
11-18-2013, 04:28 PM
Mike,

We need to compile everyone's FG kit number to reference after the data results are available.

Here is mine: FGC Kit number: 0FW1R MJost

Each completed Kit is provided many reports including a "HaplogroupCompare" report. But I have to assume it will only be a 'To Date" run. I don't know if FGC will provide updates as each kit is completed, adding a summary report back to the previously completed kit owners.

MJost

hoxgi
11-19-2013, 12:37 PM
I've got 27 now. Is this the right folks?

You can add f99512 McClure 253-1716-Mc-825 (terminal SNP PF825), who is in batch 4, apparently with results expected in the next week or two.

Greg H

hoxgi
11-19-2013, 12:41 PM
Gosh, anybody heard from David Reynolds? I was hoping he went into a hole to solve all of these problems of comparing the SNPs and lining them up... so I haven't bothered him, but I hope he is okay. Maybe he is on some big contract by one of these vendors. I just hope everything is good with him.

One of David's many roles is as one of the Z253 Project admins. David Pike and I have been including him in emails for at least 2-3 weeks without receiving a reply, which is very unlike him.

Greg H

Mikewww
11-19-2013, 12:46 PM
You can add f99512 McClure 253-1716-Mc-825 (terminal SNP PF825), who is in batch 4, apparently with results expected in the next week or two.

Greg HThanks. I'll add him to the FG list. (I have your messages on the other changes/updates for the other products too.) He's another super-explorer. We need them. I think we need to ignore the WAMH and Nialls badges and give these guys big superman "S" badges.

On David, that is worrisome. I sure hope everything is okay. I kind of half expected him to show up with a Ysearch for SNPs program or something but I'll just settle to have him back, period.

Rory Cain
11-19-2013, 08:41 PM
Thanks. I'll add him to the FG list. (I have your messages on the other changes/updates for the other products too.) He's another super-explorer. We need them. I think we need to ignore the WAMH and Nialls badges and give these guys big superman "S" badges.

On David, that is worrisome. I sure hope everything is okay. I kind of half expected him to show up with a Ysearch for SNPs program or something but I'll just settle to have him back, period.

About two years ago David was overwhelmed by his various roles as project admin of numerous projects, ISOGG representative for R-L21, etc., etc. Then suddenly it was like he disappeared into a witness protection program or something similar. When he recovered his physical and mental health he reappeared almost as if he had never been missing, with all the energy of the old David we had all come to know and to love. Based on that experience I am optimistic that he is well but recharging his batteries and we will hear from him again when he feels ready.

David Wilson
11-20-2013, 08:12 AM
Update on my FG test: The progress bar on my results page is at about 85% and is showing some red.

"David Wilson - S4C39 - Status: We sequenced your kit and are analyzing the results."

I was one of the 11 UCLA Beta testers in batch 6. I know that there is some quality control analysis to be done on these tests, but I would hope to have some kind of report within a few to several days. Somebody please correct me if this is optimistic.

David Wilson
FTDNA 8999
FGC S4C39

Rory Cain
11-20-2013, 08:33 PM
Update on my FG test: The progress bar on my results page is at about 85% and is showing some red.

"David Wilson - S4C39 - Status: We sequenced your kit and are analyzing the results."

I was one of the 11 UCLA Beta testers in batch 6. I know that there is some quality control analysis to be done on these tests, but I would hope to have some kind of report within a few to several days. Somebody please correct me if this is optimistic.

David Wilson
FTDNA 8999
FGC S4C39

Let's just say that after a 6 month wait, I'm not exactly holding my breath any more. BBut we live in hope, I suppose. I can only hope that you are right.

Mikewww
11-21-2013, 01:58 PM
My FG profile page now is showing about a 60% complete status!

Kit number: 0FW1R

MJost
Mark, do you have a list of FG kit # for each name on the list. I'll figure out a place in the spreadsheet to put them.

P.S.To all: this thread is for Full Genomes Corp test tracking, only. There are threads for other things so I'm trying to move them to keep in the right place.

kenmunn
11-21-2013, 02:17 PM
f139697 = FG: 0ANEE

Dubhthach
11-21-2013, 02:21 PM
f176148 = UFG6K

-Paul
(DF41+)

Muircheartaigh
11-21-2013, 02:50 PM
Mike. -Murta f205635 FG kit # BVZL3 batch # 5

Ray cluster 253-1716-11

RobertCasey
11-21-2013, 02:58 PM
Robert Casey - 91CZO - Status: We sequenced your kit and are analyzing the results.
Your kit is currently being processed. Batch #4 (progress bar is around 80 %).

Casey, 77349, (L226)

Celtarion
11-21-2013, 05:47 PM
Batch #5 has now been updated under the following status: We received your completed kit and are working on sending it to the lab.

I suppose that the kits have been sent to BGI for sequencing at this stage.

MJost
11-21-2013, 06:39 PM
So, we, the Full Y DNA Testers have or are about to received our long awaited results, and will soon discover that the journey is not finished yet. More work will be needed. To further this process the individual HaplogroupCompare" and other reports will be required for cross-reference and other tasks. These reports will identify your novel SNP(s) along with a number of "private" SNPs. Novel SNP(s) that are derived, and also found in other datasets, either other FGC- L21er's and/or are found in other major Y-DNA datasets.

We all want our newly discovered SNP(s) placed on the Y-DNA Tree for all to see. ISOGG now has the 'Final' word on the placement aspect. The first step in this process is that ISOGG requests one derived sample to be sequenced (=confirmed) with Sanger. This is one of several criteria required for Tree placement. This is required to make sure that it's not an artifact of the analysis method used. When this is confirmed, there will be the need for more confirmations (other methods are considered such as NGS results) from other kits within- and outside your Haplogroup group to satisfy the other criteria.

To assist in confirming validity for any new novel SNPs found in your FGC reports by further conducting the Sanger testing, I am working with a well known yet un-named "Expert" with this process who can produce the primers and run the initial SNP testing required by ISOGG. This is a US based company.

I would like to coordinate the above process for my self and other FGC Full Y testers.


MJost



f8999 Wilson 49-2329222-55717
fN3362 Maher 21-5909-1336
f226869 McGuire 513-A2-M
f228772 Reid 513- uas
f193834 Yurzaditsky 251-11EE
f148326 zzzUnk(Ross) z1130-A1-A FGC#: 0FW1R, Batch 4 @ 85%
f28714 Cain 21-246-255-658
f20437 Reynolds 21-246-255-3655-627
f129036 Harrison 49*-2526-B
f11143 Chandler z9919-A
f2224 McCeney z9919-A5
fN55408 Smith z141121
f186947 Edgcombe z9914-E
f196041 Williamson 21-5909-LS
fN36510 Fueston 21- uas
f240201 Walker 41-1426C
f176148 Duffy 41-1013 FGC#:UFG6K
f117117 Holladay 49*-1014
f258447 Taylor 1335-1065-Sc2437
f107327 Iles 1335-1065-Sc2415
f77349 Casey(SCarolina) 253-2534-226-C1 FGC#:91CZO
f22874 Irvine 251-555-Irw
fN7406 Donaldson 49-2329222- uas
f139697 Godwin 251-1124-9 FG: 0ANEE
f205635 Murta 253-1716-11 FGC# BVZL3 batch #5
f233265 Le Gall 253-2534- uas
f273282 Trainor 49-23- uas

MacUalraig
11-21-2013, 10:17 PM
Mark,

I would have thought that most of us only know one company who has such facilities? Is there a choice in the market?

But anyway I thought that either now or shortly ISOGG was going to allow alternative routes to get onto their recognised tree without requiring Sanger testing? I believe even now there is a criterion to allow it although not a very practical one.

Another question, are you suggesting people are going to want to do this for *all* their new SNPs? Just thinking out aloud here but I guess so since without more widespread comparison testing you aren't going to know the relative positions and hence which ones are worth putting on sale.

ontheedge
11-21-2013, 10:34 PM
f186947 Edgcombe z9914-E
FG: # KAQZG Batch # 5
Eddy Edgecombe

MJost
11-21-2013, 11:20 PM
Mark,

I would have thought that most of us only know one company who has such facilities? Is there a choice in the market?

But anyway I thought that either now or shortly ISOGG was going to allow alternative routes to get onto their recognised tree without requiring Sanger testing? I believe even now there is a criterion to allow it although not a very practical one.

Another question, are you suggesting people are going to want to do this for *all* their new SNPs? Just thinking out aloud here but I guess so since without more widespread comparison testing you aren't going to know the relative positions and hence which ones are worth putting on sale.

Yes there are other sources.

Using NGS new SNP finds will still need PCR testing to prove its not a False Positive or something. Most testing will first be done on novel SNPs, that is those where they have been found in other test subjects. Private SNPs will have to be further tested down the road. Lets say you find a private SNP, one that no one has yet, but in a month another tester proves positive for your private SNP then I would say you need to get it SANGER tested to validate it. The you have the mechanism to test others in future ie via the new single SNP test, or its position added to a CHIP.

The remaining private SNPs just stay in pile waiting to be matched up.

MJost

MJost
11-21-2013, 11:24 PM
[QUOTE=MJost;20360]I would like to coordinate the above process for my self and other FGC Full Y testers.


So a follow-up, I am looking for the completed FGC result files that are sent to each individual, for now. The file names contained are:

VariantCompare

haplogroupCompare

gtype


These files are contained along with others in a Zipped format. They can be forwarded directly to me for review.


I will then forward to the yet un-name company for their experts to verify and create a primer and submit payment to validate the new

novel SNP found as the first step in the process of getting it on the ISOGG tree. From these files I will be able to evaluate which

other FGC returned kits contain either an ancestral or derived states. Additional testing of others maybe required. Example would be

if you are currently DF13* and it reports that four DF13 subclades indeed have the referenced ancestral allele, then only the

remaining ISOGG subclades will need to be tested.

Remember these steps are needed to prove that the new novel SNP is valid and further correctly placed on the Tree.


MJost

LarryWalker
11-22-2013, 08:28 PM
I've posted my "Variant Compare" spreadsheet online for the curious at http://rangebiome.org/FG-SNP1.xlsx , and forwarded the whole enchilada to Mark.:beerchug:

Rory Cain
11-28-2013, 01:17 AM
[QUOTE=MJost;20360]I would like to coordinate the above process for my self and other FGC Full Y testers.


So a follow-up, I am looking for the completed FGC result files that are sent to each individual, for now. The file names contained are:

VariantCompare

haplogroupCompare

gtype


These files are contained along with others in a Zipped format. They can be forwarded directly to me for review.

MJost

I would be quite happy to forward these files I received if I actually knew what was in them. But my Mac cannot open whatever obscure program FGC use (except the ".txt" files which open OK. Consequently I feel quite reluctant to forward something for wider consumption by lucky folks inside the nice warm restaurant when I am locked outside. I suspect there is nothing in them that I wouldn't share, but I don't actually know that until Mac finds a way to open them. The reason why I didn't go direct to BGI when I heard about their excellent work in agricultural DNA sequencing 2 years ago was that I wanted an English speaking company that dealt in human DNA as I figured the analysis report would still be the most valuable part. It has been valueless to date. Any Mac users have any ideas?

MJost
11-28-2013, 03:48 AM
The Out and Tab extension files are Tab Delimited and can be opened by Microsoft Excel or Open Office. When you open it it will set up a Delimit conversion window. In the Separate section, check the Tab box and leave the Space box checked. Click Finish. It will now populate the Cells with the data.

http://sourceforge.net/projects/openofficeorg.mirror/files/4.0.1/binaries/en-US/Apache_OpenOffice_4.0.1_MacOS_x86_install_en-US.dmg/download

Rory, please forward me your zipped file for review and I can then convert it for you if you need.

MJost

MJost

Rory Cain
11-28-2013, 04:05 AM
The Out and Tab extension files are Tab Delimited and can be opened by Microsoft Excel or Open Office. When you open it it will set up a Delimit conversion window. In the Separate section, check the Tab box and leave the Space box checked. Click Finish. It will now populate the Cells with the data.

http://sourceforge.net/projects/openofficeorg.mirror/files/4.0.1/binaries/en-US/Apache_OpenOffice_4.0.1_MacOS_x86_install_en-US.dmg/download

Rory, please forward me your zipped file for review and I can then convert it for you if you need.

MJost

MJost

Problem solved, thanks to a simple solution from Greg Magoon, i.e. change the ".out" and ".tab" endings to ".csv" and the files then become Mac Numbers/ MS Excel compatible. I'm still happy to email my results if you wish for research purposes. What I can see so far is that I have 36 new SNPs numbered FGC5752 to FGC 5787, and eight new InDels numbered FGC5788 to FGC5795. Plus I had three unexpected results in P108-, P305_ and V221- which were all expected to be positive, but are not. Back mutations?

In the area of shared SNPs, I have the three that David Reynolds reported in his results as lying between Z246 and CTS3655, namely 5185401G->A, 9129841T->G and 8381834C->G (now accepted as FGC3899, FGC3900 and FGC3903 respectively. I wonder if Alex Williamson has all or some of these? Regrettably L1446 & L1447 found in other DYS442=11 & DYS450=9 folks were not reported so may have been negative or else no calls.

George Chandler
11-29-2013, 06:18 PM
Here is another, from our illustrious leader no less. George, I'm pretty sure he is just really busy. I certainly hope that's it. I've heard rumors of various projects he is working on. They are just rumors but that would account for a lot of extra activity for him.

f20437 Reynolds R1b-P312>L21>DF13>DF21>Z246>DF25>DF5>CTS3655>L627>L626+ 3c1.3g 21-246-255-3655-627

http://www.anthrogenica.com/showthread.php?170-DF21-(L21-gt-DF13-gt-DF21)-and-Subclades-(DF5-S191-P314-2-S190-etc)&p=16622&viewfull=1#post16622

Is there anyone else who has received FGS results (and is located under L21) and able to post their position, kit numbers and list of high quality SNP's for the group?


Thanks
George

Mag Uidhir 6
11-30-2013, 03:05 AM
Is there anyone else who has received FGS results (and is located under L21) and able to post their position, kit numbers and list of high quality SNP's for the group?


Thanks
George

George, expecting one R-L513>L69.5+ test in a few weeks....Jan? Feb??? Unk.

When rcvd, will post here.

Brad

Dubhthach
11-30-2013, 03:34 AM
Once I receive mine I'll be posting them as well -- Batch 5 (DF41+)

Celtarion
11-30-2013, 09:49 AM
Waiting for mine... So I'll provide the results as well. Batch 5 (L21>Z253>Z2534*)

hoxgi
11-30-2013, 11:55 PM
It appears that FGC are changing the designations of private SNPs discovered in the early FG tests, so that all such SNPs will have a designation prefixed by FGC rather than FG. As part of this process, the numerals after the prefix have also been changed.

Perhaps those who have posted their new SNPs for L21+ kits could provide updated results on this thread.

Here are the changes for McClure PF825+:

new SNPs (95-99% reliability) FG1572-FG1619 changed to FGC3221-FGC3268 and three private indels now designated FGC3269, FGC3270 and FGC3217 (hopefully the last is not a typo).

So McClure still has no shared new SNPs with Robert Casey, although both are Z253+.

Greg H

hoxgi
12-01-2013, 10:10 AM
Update on FG results of McClure Z253+ PF825+.

He does match some new FG SNPs and these are listed with all his other positive SNPs, not with his private SNPs (of course - because they are not private).

After a bit of trial and error, I think the best approach for a non-expert such as me is just to open the HaplogroupCompare file in an Excel spreadsheet (which I had to do via Notebook for some reason) and scroll down column E, which lists the SNPs. Column F gives the reliability rating (number of asterisks) and column G the results of the person whose DNA has been analyzed.

Columns H to AH give comparisons with reference kits from the 1000 Genomes Project and Personal Genomes Project. In McClure's case these have been selected so that all reference kits are L21+ and more than half are DF13+, although some have not tested for DF13. Ten of the references are Z253+, including one from the Personal Genomes Project which is Z2534+.

So, restricting ourselves to no or one asterisk results (95-99% reliability), McClure is positive for FGC13-FGC30, FGC62, FGC83, FGC186, FGC187 and FGC330 (making 23 SNPs previously discovered in Full Genomes tests of others).

He also is positive for FGC3218, FGC3219 and FGC3220 in his list of non-private SNPs. FGC3218 is positive in all but one of the reference kits which have tested for it. FGC3219 is negative in all the reference kits but must have been found elsewhere as it is not listed as a private SNP. FGC3220 is present in only one of the reference kits, a Z253+ one from the 1000 Genomes Project.

Anyone else have one of the above FGC SNPs ?

Greg H

George Chandler
12-01-2013, 06:50 PM
It appears that FGC are changing the designations of private SNPs discovered in the early FG tests, so that all such SNPs will have a designation prefixed by FGC rather than FG. As part of this process, the numerals after the prefix have also been changed.

Perhaps those who have posted their new SNPs for L21+ kits could provide updated results on this thread.

Here are the changes for McClure PF825+:

new SNPs (95-99% reliability) FG1572-FG1619 changed to FGC3221-FGC3268 and three private indels now designated FGC3269, FGC3270 and FGC3217 (hopefully the last is not a typo).

So McClure still has no shared new SNPs with Robert Casey, although both are Z253+.

Greg H

Hi Greg,
If the naming of newly discovered SNP's FG1572-FG1619 have been changed (not only the prefix but the numbers as well) to FGC3221-FGC3268 then it messes up all the newly discovered data.

George

George Chandler
12-01-2013, 07:01 PM
Update on FG results of McClure Z253+ PF825+.

He does match some new FG SNPs and these are listed with all his other positive SNPs, not with his private SNPs (of course - because they are not private).

After a bit of trial and error, I think the best approach for a non-expert such as me is just to open the HaplogroupCompare file in an Excel spreadsheet (which I had to do via Notebook for some reason) and scroll down column E, which lists the SNPs. Column F gives the reliability rating (number of asterisks) and column G the results of the person whose DNA has been analyzed.

Columns H to AH give comparisons with reference kits from the 1000 Genomes Project and Personal Genomes Project. In McClure's case these have been selected so that all reference kits are L21+ and more than half are DF13+, although some have not tested for DF13. Ten of the references are Z253+, including one from the Personal Genomes Project which is Z2534+.

So, restricting ourselves to no or one asterisk results (95-99% reliability), McClure is positive for FGC13-FGC30, FGC62, FGC83, FGC186, FGC187 and FGC330 (making 23 SNPs previously discovered in Full Genomes tests of others).

He also is positive for FGC3218, FGC3219 and FGC3220 in his list of non-private SNPs. FGC3218 is positive in all but one of the reference kits which have tested for it. FGC3219 is negative in all the reference kits but must have been found elsewhere as it is not listed as a private SNP. FGC3220 is present in only one of the reference kits, a Z253+ one from the 1000 Genomes Project.

Anyone else have one of the above FGC SNPs ?

Greg H

Justin confirmed that all previous new FG SNP's were changed - thanks for posting that update.

George

Rory Cain
12-02-2013, 02:08 AM
Update on FG results of McClure Z253+ PF825+.

So, restricting ourselves to no or one asterisk results (95-99% reliability), McClure is positive for FGC13-FGC30, FGC62, FGC83, FGC186, FGC187 and FGC330 (making 23 SNPs previously discovered in Full Genomes tests of others).

He also is positive for FGC3218, FGC3219 and FGC3220 in his list of non-private SNPs. FGC3218 is positive in all but one of the reference kits which have tested for it. FGC3219 is negative in all the reference kits but must have been found elsewhere as it is not listed as a private SNP. FGC3220 is present in only one of the reference kits, a Z253+ one from the 1000 Genomes Project.

Anyone else have one of the above FGC SNPs ?

Greg H

Greg, I am DF21+ L658+ and have some of the above SNPs you ask about: FGC13-29, FGC62, FGC83and FGC3218. I recall some-one commenting on line that DF21 and Z253 are so close that they likely share a common SNP somewhere upstream. However we need to see whether DF21- and Z253- kits also share these SNPs.

Rory

Rory Cain
12-02-2013, 03:58 AM
Greg, I am DF21+ L658+ and have some of the above SNPs you ask about: FGC13-29, FGC62, FGC83 and FGC3218. I recall some-one commenting on line that DF21 and Z253 are so close that they likely share a common SNP somewhere upstream. However we need to see whether DF21- and Z253- kits also share these SNPs.

Rory

Also add FGC186 and FGC330. In fact my shared FGC SNP list is almost identical with the SNPs Greg listed except I also have FGC67, FGC1557 & 1558 what approximate DF21, and FGC3899, 3900 & 3903 which are between Z246 and CTS3655.

Williamson
12-03-2013, 05:53 AM
So, restricting ourselves to no or one asterisk results (95-99% reliability), McClure is positive for FGC13-FGC30, FGC62, FGC83, FGC186, FGC187 and FGC330 (making 23 SNPs previously discovered in Full Genomes tests of others).

He also is positive for FGC3218, FGC3219 and FGC3220 in his list of non-private SNPs. FGC3218 is positive in all but one of the reference kits which have tested for it. FGC3219 is negative in all the reference kits but must have been found elsewhere as it is not listed as a private SNP. FGC3220 is present in only one of the reference kits, a Z253+ one from the 1000 Genomes Project.


Hi Greg,

I've taken a look at my own FGC results, as well as those of David Reynolds and Rory Cain. We're all within R-DF21.

With regard to FGC13-FGC30, FGC62, FGC83, FGC186, FGC187 and FGC330 (the 23 SNPs you mentioned), some of us don't have a result for a couple of them, but at least one of us is positive for all of them. Furthermore, we also have FGC1556-FGC1558 and FCG67-FGC68 in our shared results as well, although we are all ** for FGC1558. By the look of the huge list of samples sharing the variant (from the variant compare file), all these SNPs are well above L21, and we should all be positive for them. This agrees with what Rory said as well.

With regard to FGC3218-3220, neither of the 3 of us have FGC3219 or FGC3220, so I can't say anything at all. However, it looks as though all 3 of us are positive for FGC3218. My result wasn't given, but looks to be positive based on my BAM file. Furthermore, the list of sample variants seems to coincide with the R-L21 kits from 1000 Genomes, and perhaps PGP as well (I didn't check). I'd say FGC3218 is equivalent to L21. What is the reference listed as negative for this SNP?

Thanks,
Alex

hoxgi
12-03-2013, 01:35 PM
Hi Alex

That's an interesting set of results. The reference which is FGC3218- is PGP40 from the Personal Genomes Project. PGP40 is L21+ DF13+ Z253-, which places FGC3218 below DF13, assuming the results are accurate. Several of the other references have a ? result for FGC3218, so presumably FGC3218 was not tested.

FGC3218 was derived in the following references:
OFW1RA (DF13+)
NA19717 (Z253+)
HG00105 (Z253+)
HG01136 (Z253+)
HG01079 (L21+)
NA12045 (DF13+)
NA19658 (L21+)
HG01953 (DF13+)
HG00115 (DF13+)
HG00119 (L21+)
HG01405 (Z2534+)
HG01675 (Z2534+)
PGP106 (Z253+)
PGP61 (DF13+)
PGP50 (DF13+)
PGP151 (DF13+)
PGP126 (L144.1+)
NA12335 (DF13+)
PGP101 (Z2534+)

So it looks as though FGC3218 is probably above Z253 but below DF13 at this stage. Anyone else who has FG results and is DF13+ should check their HaplogroupCompare file for this SNP.

Greg H

MacUalraig
12-03-2013, 02:11 PM
I am FGC3218+ and R1b-M222.

MacUalraig

Dubhthach
12-03-2013, 02:27 PM
I could be mistaken here but Larry Walker who is DF41+ appears to be: FGC3218+

This is going by the spreadsheet that he posted in the DF41 yahoo group.

-Paul
(DF41+)

RobertCasey
12-03-2013, 03:10 PM
I think I have now discovered how to analyze Full Genomes submissions. Here are the steps:

1) The gtype file is the best and easiest way to determine assigned YSNPs other than FGC novel discoveries. This yielded 12 possible new L21 YSNPs when I compared
P312/DF99, Z253/L226 and Z253/DF825. Looking at the compare files for these YSNPs do not add any new information.
2) For novel Full Genomes files, I plan on using the following methodology and then create a cross reference to FGC numbers (will not use any FG numbers since they are being replaced with new numbers in addition to a new prefix):

FSS - FG Shared SNP + YChr position
FSI - FG Shared Indel + YChr position
FPS - FG Private SNP + YChr position
FPI - FG Private Indel + Ychr position

The P312/DF99 has no assigned FG or FGC numbers for now. The Z253/DF825 only has FG numbers and an email stating new FGC numbers recently sent via an update - impossible to assign to YChr numbers for ones that do not match my results and can not be compared to our baseline P312/DF99. All submissions have many high quality shared mutations that are not assigned any FGC numbers which need to be tracked for L21. It now appears that all private YSNPs and indels are now receiving FGC assignments but older results files do not have these assignments. I am trying clean up my comparison spreadsheet and will post FG novel YSNPs sometime tonight. I am ready to review a couple of non-Z253 submissions, so if you want an analysis of your results, send your original email with results to me and I will post the comparison summary with the other three submissions. If you want my original files for your own comparison, let me know and I will forward my results to you. Also, if you have received any FG updated files, send those as well:

http://www.rcasey.net/DNA/R_L21/R_L21_Contact_Project.html

Here is the current analysis of the YSNPs that already have YSNP assignments that are not novel YSNPs discovered by FG (CTS, PF, K, L, M and Z):

http://www.anthrogenica.com/showthread.php?1651-Methodology-of-determining-new-Full-Genomes-YSNPs-P312-L21

Williamson
12-04-2013, 01:43 AM
The R-DF63 men HG02014 and HG00243 are also positive for FGC3218, so this SNP can't be any lower down than L21. As I mentioned above, I also don't see any men outside of R-L21 listed as positive for this SNP on my report, so I do think it is likely equivalent to L21. If PGP40 is negative for this SNP, perhaps it's an error, or perhaps it a back mutation.

Alex

bmcceney
12-04-2013, 02:07 PM
Mark, do you have a list of FG kit # for each name on the list. I'll figure out a place in the spreadsheet to put them.

P.S.To all: this thread is for Full Genomes Corp test tracking, only. There are threads for other things so I'm trying to move them to keep in the right place.


Mike,

My FGC kit was sent to the lab today 12-4-13 in batch #5.

9919-5
VKDDD, Batch #5
Bill McCeney

Williamson
12-05-2013, 03:10 AM
Mark is compiling a database from the haplogroupCompare files, and Robert is compiling a database from the gtype files. In what is surely a sign of my poor judgement, I actually like the variantCompare files.

What I haven't seen available online so far is a big spreadsheet with FullGenomes results. As, such I propose to put one up. In fact, I already have. You can find it at:

http://www.littlescottishcluster.com/RL21/Files/SNPs.xlsx

In this file, I have taken the results from the 3 FGC tests I have available to me so far (all R-DF21), and included all the information from the variantCompare files. The spreadsheet is organized with SNPs down the left, and tested men across the top (just 3 so far). The SNPs are organized by position, rather than SNP name. SNP names seem to be far to confused for me to try and use them.

For each man I give their SNP results with confidence levels as presented by FGC. Actually, I've changed the blank confidence level to 0, because I worry blank might be interpreted as unknown, and it's easier because I VLOOKUP the results. For those SNPs that I can't find in someone's results, I put "NR", meaning no result. It might be positive, it might be negative, we just don't know. The ** and *** results are included as well.

At the present time, I also have a number of other columns on the spreadsheet as well. Some of these columns may stay in the future and some may go. I don't know what the best format is yet. One of these columns is "Samples sharing variant", which lists the 1000 genomes, and PGP men which share the SNP. This is really handy in determining where a SNP is on the Y tree. Those SNPs comparable to L21 or DF13 typically have about 40-60 listed men. There is a count of the names in the next column. Those SNPs (and INDELs) for which at least one man is 0 or 1 star (*) can be filtered on in the last column.

Now I understand that we really don't need 3 people keeping track of the FGC results. I think it is safe to say however that we don't yet know what the best way really is. I'll keep track of the records this way until it becomes far too laborious to keep them, or until it is obviously a poor way to organize the information.

As always, I welcome any suggestions or criticisms. Anyone wishing to have their R-L21 FGC results included in the file, just needs to e-mail me their results. I'm not sure how big the file will become over time, but we'll find out. Once the avalanche of Big Y results become available, perhaps they can be included in this format as well if the SNP positions can be determined.

As per Robert's advice, my e-mail address is below as a picture.

1008

Alex

RobertCasey
12-05-2013, 04:32 PM
Glad to see another excellent review of three more submissions. Here are some observations comparing our two methodologies:

1) I omitted all lower quality YSNPs in my FGC YSNP analysis. I can see from your spreadsheet that this could be a mistake as I could be filtering out test results. So I need to go back for my FGC YSNPs and keep all of them.
2) I am convinced that the gtype file is the only reliable source for non-FGC YSNPs and the compare file is the only source for FGC YSNPs (see how adding gtype file information filled in so many missing non-FGC YSNPs in my updated post that was missing in the Compare file). The list below shows that many other FGC YSNPs are not listed as positive when they must be positive (could be my filtering out of lower quality results - also I only received the updated PF825 file last night and need to go through the new file again).
3) We now know that not listed does not equate to negative. PF5888 was verified to be pre-P312 via Nat Geo testing but was not listed in the P312/DF99 compare file (but was found in the gtype file as PF5888+). You found conflict in the BAM file
and the Compare file (but Warwick stated that the read was not reliable enough to be called ?). So we will depend more on getting pre-Z253 and pre-DF21 where additional positive results show that many YSNPs are upstream of our focus.
4) You need to get the updated file for the Reynolds FG SNPs as there could be some more overlap discovered since the numbers will change.

I compared your FGC YSNPs to my three YSNPs positives are listed that are shared:

FGC28 - DF21(3), PF825 - Approx DF13 - L226 is probably positive as well but not listed
FGC148 - DF99, L226, DF21(3) - Approx P312 - PF825 is probably positive but not listed
FGC164 - L226, PF825, DF21(3) - Approx DF13
FGC173 - DF99, L226, DF21(3) - Approx P312- PF825 is probably positive but not listed
FGC267 - L226, DF21(3) - Approx DF13 - PF825 is probably positive but not listed
FGC271 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed
FGC385 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed
FGC1556 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed
FGC1557 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed

Alex, if you send me your zip file, I will send you my zip file (be sure to include update files). We need to verify with the others that it is OK to share their files with others (as well as publicly post any results):

http://www.rcasey.net/DNA/R_L21/R_L21_Contact_Project.html

We really need some L21** and DF13** results to sort out the pre-DF21 and pre-Z253 YSNPs. The P312/DF99 did help on FGC173 and FGC148 as being pre-L21 (I was hoping for more filtering than just two).

warwick
12-05-2013, 04:40 PM
3) We now know that not listed does not equate to negative. PF5888 was verified to be pre-P312 via Nat Geo testing but was not listed in the P312/DF99 compare file (but was found in the gtype file as PF5888+). You found conflict in the BAM file
and the Compare file (but Warwick stated that the read was not reli

To clarify, Greg is not calling that SNP because the number of reads in the raw data did not meet our threshold, i.e. too few reads in the BAM file. Based on other near neighbors it can be called, but we don't call unless the SNPs have a higher level of confidence in the raw data, to avoid false positives.

LarryWalker
12-05-2013, 05:18 PM
Alex, if you send me your zip file, I will send you my zip file (be sure to include update files). We need to verify with the others that it is OK to share their files with others (as well as publicly post any results):

http://www.rcasey.net/DNA/R_L21/R_L21_Contact_Project.html



You and everybody else have my permission, FG kit 29FKD. The more public the better as DNA data that is not widely shared is next to worthless even to its owner.

RobertCasey
12-05-2013, 05:30 PM
To clarify, Greg is not calling that SNP because the number of reads in the raw data did not meet our threshold, i.e. too few reads in the BAM file. Based on other near neighbors it can be called, but we don't call unless the SNPs have a higher level of confidence in the raw data, to avoid false positives.

So, there will be scenarios that due to the quality of the individual test, that some YSNPs will not meet the required quality threshold and therefore will not be reported to avoid false positives. However, later Sanger testing could test positive for a few YSNPs, so this could also be miss of a positive. By looking at the BAM file directly, you may see some evidence that it could test positive but since the results were too inconsistent with 50X coverage & 100 read length, it is not reported as positive.

Is there any way to determine if FGC YSNPs have tested negative and generate a report of known FGC YSNPs ? This would be very useful, otherwise, we have the Nat Geo 2.0 upload issue again of meaningful negatives that are not reported. I would hate to have some of us looking at all the BAM files for negatives that could be reported. I know that this is a moving target as new FGC YSNPs are discovered weekly, but an occasionally update with negative updates would be very useful and save on a lot on post FG testing via individual testing of YSNPs.

warwick
12-05-2013, 05:46 PM
So, there will be scenarios that due to the quality of the individual test, that some YSNPs will not meet the required quality threshold and therefore will not be reported to avoid false positives. However, later Sanger testing could test positive for a few YSNPs, so this could also be miss of a positive. By looking at the BAM file directly, you may see some evidence that it could test positive but since the results were too inconsistent with 50X coverage & 100 read length, it is not reported as positive.

Is there any way to determine if FGC YSNPs have tested negative and generate a report of known FGC YSNPs ? This would be very useful, otherwise, we have the Nat Geo 2.0 upload issue again of meaningful negatives that are not reported. I would hate to have some of us looking at all the BAM files for negatives that could be reported. I know that this is a moving target as new FGC YSNPs are discovered weekly, but an occasionally update with negative updates would be very useful and save on a lot on post FG testing via individual testing of YSNPs.

All that be required would be the creation of an FGC snp report with confidence calls for all the FGC SNPs. Keep in mind that if you include a low confidence SNP that requires a judgement that it is plausible to include it, based on that sample.

For example, my original sample in the 5 sample pilot study had 36 private SNPs according to one analysis but we refined that down to 24 upon development of better criteria.

warwick
12-05-2013, 06:01 PM
I know that this is a moving target as new FGC YSNPs are discovered weekly, but an occasionally update with negative updates would be very useful and save on a lot on post FG testing via individual testing of YSNPs.

I would not personally advocate additional Sanger sequencing for testees, since these issues can be resolved.

RobertCasey
12-05-2013, 08:16 PM
I would not personally advocate additional Sanger sequencing for testees, since these issues can be resolved.

I believe that Mark Jost stated that ISOGG requires any new YSNP has to be Sanger sequenced as part of ISOGG qualification. I assume that the Krahn's test would be Sanger testing. Not sure if FTDNA single YSNP tests are still Sanger tested. I did request that five FGC YSNPs be added at YSEQ and also filled out the YSNP forms for FTDNA as well. FGC164 (shared by L226 and DF825 submission), FGC498 (only high quality YSNP for L226 submission that has a lower number listed which is probably shared with an earlier unknown FG tester). I also added three more L226 only FGC YSNPs to have some random testing just under and just above L226 (all 99 % reliable).

With six tests being compared - FGC164 is positive for Z253 and DF21, so it has moved up to approximate DF13. FGC498 did not show positive for any DF21 test or the PF825 test. So another Z253 test must have results FGC498, if so, this would make FGC498 Approx Z253. This assumes that PF825 is really negative for FGC498 which has some risk. The other three are L226 only and are probably Approx L226.

warwick
12-05-2013, 08:18 PM
I believe that Mark Jost stated that ISOGG requires any new YSNP has to be Sanger sequenced as part of ISOGG qualification. I assume that the Krahn's test would be Sanger testing. Not sure if FTDNA single YSNP tests are still Sanger tested. I did request that five FGC YSNPs be added at YSEQ and also filled out the YSNP forms for FTDNA as well. FGC164 (shared by L226 and DF825 submission), FGC498 (only high quality YSNP for L226 submission that has a lower number listed which is probably shared with an earlier unknown FG tester). I also added three more L226 only FGC YSNPs to have some random testing just under and just above L226 (all 99 % reliable).

With potentially 40,000 new SNPs I'm not sure that this will be feasible. [across all haplogroups and potentially combined total tests across companies]
[100+ SNPs in some J samples for example and 200+ in some G samples alone]

Williamson
12-06-2013, 06:07 AM
Glad to see another excellent review of three more submissions. Here are some observations comparing our two methodologies:

1) I omitted all lower quality YSNPs in my FGC YSNP analysis. I can see from your spreadsheet that this could be a mistake as I could be filtering out test results. So I need to go back for my FGC YSNPs and keep all of them.
2) I am convinced that the gtype file is the only reliable source for non-FGC YSNPs and the compare file is the only source for FGC YSNPs (see how adding gtype file information filled in so many missing non-FGC YSNPs in my updated post that was missing in the Compare file). The list below shows that many other FGC YSNPs are not listed as positive when they must be positive (could be my filtering out of lower quality results - also I only received the updated PF825 file last night and need to go through the new file again).
3) We now know that not listed does not equate to negative. PF5888 was verified to be pre-P312 via Nat Geo testing but was not listed in the P312/DF99 compare file (but was found in the gtype file as PF5888+). You found conflict in the BAM file
and the Compare file (but Warwick stated that the read was not reliable enough to be called ?). So we will depend more on getting pre-Z253 and pre-DF21 where additional positive results show that many YSNPs are upstream of our focus.
4) You need to get the updated file for the Reynolds FG SNPs as there could be some more overlap discovered since the numbers will change.

I compared your FGC YSNPs to my three YSNPs positives are listed that are shared:

FGC28 - DF21(3), PF825 - Approx DF13 - L226 is probably positive as well but not listed
FGC148 - DF99, L226, DF21(3) - Approx P312 - PF825 is probably positive but not listed
FGC164 - L226, PF825, DF21(3) - Approx DF13
FGC173 - DF99, L226, DF21(3) - Approx P312- PF825 is probably positive but not listed
FGC267 - L226, DF21(3) - Approx DF13 - PF825 is probably positive but not listed
FGC271 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed
FGC385 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed
FGC1556 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed
FGC1557 - L226, DF21(3) - Approx DF13- PF825 is probably positive but not listed

Alex, if you send me your zip file, I will send you my zip file (be sure to include update files). We need to verify with the others that it is OK to share their files with others (as well as publicly post any results):

http://www.rcasey.net/DNA/R_L21/R_L21_Contact_Project.html

We really need some L21** and DF13** results to sort out the pre-DF21 and pre-Z253 YSNPs. The P312/DF99 did help on FGC173 and FGC148 as being pre-L21 (I was hoping for more filtering than just two).

Hi Robert,

Thanks for the comparison.

I have updated my online spreadsheet with Larry Walker's results. Fortunately (from an storage perspective), and as expected, the addition of his data didn't require as many new rows as the earlier results. As more and more results are included from R-L21, we should find fewer and fewer novel SNPs.

I will have to create a proper webpage for the analysis, with a proper link to the spreadsheet. That should appear in the next few days.

For now, the link is:

http://www.littlescottishcluster.com/RL21/Files/SNPs.xlsx

There is also a link to the file on the "Other Sites" page of my LittleScottishCluster.com site,

http://www.littlescottishcluster.com/othersites.html

In addition to adding Larry's information, I've also updated to the FGC names of David Reynold's SNPs. The previous version of the file had the FG names.

One feature I like in the variantCompare file that the gtype file lacks is the huge list of 1000 genomes and PGP samples that also share the SNP (or INDEL). As such, I think we can say a lot more about many of the shared FGC SNPs that have been discovered so far.

If you look at the above spreadsheet, I have it filtered on column K as True, which picks out SNPs (or INDELs) for which at least one man is 0* or 1*. Although you may wish to relax this constraint, it does allow one to concentrate on the most likely SNP candidates. I have also sorted it by shared/private SNPs/INDELs, and then by the number of 1000 genomes or PGP samples in decreasing order.

The top SNPs are shared with over 1000 samples from across much of the Y-Tree. Thus we know they are well above L21 (Above from the perspective of Mike Walsh's famous SNP diagrams), and really not that interesting from an R-L21 perspective. As we go down the list, we eventually come to the L21 and DF13 level SNPs. These SNPs are shared by about 40-60 of the 1000 genomes/PGP samples. Further down the list the counts drop significantly, and these are the private SNPs which are from the DF21, DF41, etc. clades.

To summarize the status of the widely shared FGC SNPs and INDELs, I'd say:


FGC13-30, FGC62, FGC67-68, FGC83, FGC186-187, FGC330 and FGC1556-1558 are all likely above L21. That is 28 SNPs. FGC1558 is a little unusual in this list at the 4 men I have are all ** for this SNP.
FGC144-169, FGC173, FGC267, FGC271, FGC385 and FGC1734 are all shared INDELs that are also likely above L21. There are 31 of them.
FGC3218 is perhaps the first interesting shared SNP. It looks to be equivalent to L21. I'd like to see this one available for testing.


Not mentioned in the list above is FGC3177, which although shared by 13 other 1000 genomes and PGP men is not really a widely shared SNP. In fact, it looks to be a recurrent SNP. It appears in my line, but also in haplogroups D, H, and J2b. All of the other FGC SNPs in the spreadsheet are shared by only a handful of men so far, and belong only to the lower down clades in our R-L21 tree.

As I mentioned before, please send you FGC results (all files) to me if you'd like them included in the above spreadsheet. You should also send them to Robert and Mark, as we've taken different approaches to the analysis. Ideally, with everyone's permission, it would be great if we could simply share the files.

1016

Thanks,
Alex

Rory Cain
12-10-2013, 01:46 AM
FGC3218 is perhaps the first interesting shared SNP. It looks to be equivalent to L21. I'd like to see this one available for testing.
[/LIST]
Alex

Alex, little was flowing through from FGC testing and it looked like a repeat of the HuGO and the Irish Human Genome sequencing results which produced headlines but nothing for the enthusiasts. You have put some news out there in the public domain and I thank you for your efforts. I also thanks those individual testers who generously shared their results and ignored the privacy freaks who contribute so little. Given the effort you have put in, I am reluctant to offer criticism. I might add a few other SNPs of public interest though, for just as FGC3218 near L21 may split L21 or P312; also FGC1556, 1557 & 1558 somewhere near DF21 and FGC3899, 3900 & 3903 somewhere between Z246 and CTS3655 (and its brothers) may also be worth testing if made available. Again, thank you for converting raw data into something of interest to the wider DNA community.

Rory

MJost
12-11-2013, 08:18 AM
As most know, I have been testing my DNA since Jun 3, 2008 starting with Genebase Y-DNA 44 Marker + mtDNA HVR-1 test attempting to confirm my suggested paternal lineage. This didn't quite work out initially. Thanks to Rich Stevens, Admin of the R-L21 Plus Project suggesting further additional STR and SNP testing with Family Tree DNA led me to today's announcement.

I am R-L21>DF13*, negative for most subclades. I am FGC Kit 0FW1RA and it now appears that I have new DF13 Subclade SNP named FGC5496 as recently reported by Thomas Krahn on the 'International Society of Genetic Genealogy (ISOGG)" Group on Facebook, was discovered using next generation sequencing technology from my Comprehensive Y-DNA Sequencing service provider, Full Genomes Corporation (FGC) located in Rockville, MD. FGC was started and is headed up by Justin Lowe. Justin is working with Dr. Greg Magoon, Ph.D., Chemical Engineering, Massachusetts Institute of Technology, who has developed "next-generation" sequence data analysis tools, is providing variant and haplogroup analysis that includes "Reliability index" ratings for newly SNPs uncovered during the sequencing process.

I received my FGC results on Nov 21, 2013. I was notified by Dr. Magoon, that I have two new derived SNPs in common with a public DF13 Reference dataset now named FGC5495 and FGC5496. Thank you Justin and Greg and all the other FGC consultants.

The overall testing process was not complete though, as certain verification tests are required to be conducted for other later purposes. I would like to thank Thomas and Astrid Krahn of YSeq.net for their valuable professional expertise in providing a very quick turnaround performing the Sanger DNA primer development and sequencing required to validate a select few of my new NextGen sequenced SNPs, confirming that they are not an artifact of the analysis method used, as per ISOGG Listing Criteria for possible SNP Inclusion into the ISOGG Y-DNA Haplogroup Tree.

It has been stated, the "SNP Tsunami" is coming. In my case, I have 65 new 'Private' SNPs with 64 that have a "Reliability" level better than 90% as per Dr. Magoon's report. These levels are: 99% - 40 SNPs, 95% - 24 SNPs and 10% - 1 SNP.

In addition to the two shared Public SNPs, FGC5495 and FGC5496, 41 from my 'Private' list of 65 SNPs were chosen for review to consider further testing opportunities from which 20 were chosen based on their 'Stable Region' locations and if Astrid Krahn was able develop 'Primers' easily. I placed my order for these 22 SNPs to be tested. My DNA sample was received and was pre-processed prior to the delivery of these ordered developed primers.

Yesterday, Dec 10th, my YSEQ results were sent to me. 17 of the 22 were confirmed derived and five failed due to various reasons. One of these SNPs that had a failed primer is located in position that Thomas states that "it is likely this sequence region is nowhere on the human reference sequence. but nowhere (do) we have a really good match." I will let Thomas provide more details concerning this one. Of the two SNPs that were found within a public dataset, one SNP, FGC5495, showed an 98% identical X match and thus, no doubt, would fail, and I wanted it tested to confirm either way. This and the other SNP primer failures maybe reviewed later.

MY FGC5496 is negative in the following FGC and other Public Kits as per Greg's "Haplogroup Compare" analysis.

MRD4PA (R-DF49) R1b1a2a1a2c1a DF49/S474 MRD4PA
NA12399 (R-DF1) R1b1a2a1a2c1b DF1/L513/S215
HG00246 (R-S219) R1b1a2a1a2c1e Z255/S219
PY5HUA (R-S218) R1b1a2a1a2c1f Z253/S218 PY5HUA
P9UH4A (R-DF21) R1b1a2a1a2c1g DF21/S192 P9UH4
29FKDA (R-CTS2501) R1b1a2a1a2c1i DF41/S524/CTS2501 29FKD
NA11831 (R-Z251) R1b1a2a1a2c1j Z251
NA20278 (R-CTS4466) R1b1a2a1a2c1l CTS4466

Additional testing may be needed for current unverified DF13 Subclades
R1b1a2a1a2c1c L96
R1b1a2a1a2c1d L144.1/S175, L195/S354
R1b1a2a1a2c1h L371/S300
R1b1a2a1a2c1k L1335/S530 (two know FGC kits testing in progress)
R1b1a2a1a2c1m CTS2457.2
R1b1a2a1a2c1n L679

I have my STRs tested out to 111 and have several genealogical time frame matches that are a GD5/111 and GD8/111, and one GD13/111 which I will suggest considering they testing for FGC5496, along with the remainder unverified DF13 subclades, and to determine the depth and breadth of this new Subclade which I feel at this time, appears to be a older R-DF13 subclade. Current DF13* should consider testing for this new SNP. Mike Walsh has categorized many haplotypes into a variety nomenclature system with whom I will work closely with to assist in the above goals.

Thanks to all involved to date, as I believe I should now have a place on the ISOGG R Tree shortly.

MJost

Mag Uidhir 6
12-11-2013, 02:55 PM
Mark,

That is awesome news indeed! Love the quote too: " I should now have a place on the ISOGG R Tree shortly." From a genetic genealogist standpoint, this is the gold standard....well, along with establishing a verified paper trail to coincide. Meanwhile, your news is the best I've heard yet from FGC (anticipation for our Airghialla Mag Uidhir kit is growing by the day!!)
Brad

MJost
12-11-2013, 05:25 PM
Brad,

Thanks.

I have keep this news close to the vest as I have been disappointed so much over the years, trying to validate my DF13 subclade status. I wanted to validate this new FGC6496 SNP via the specific Sanger sequencing method first. As it was, one (FGC5495) of the two novel SNPs failed the SNP test initially leaving FGC5496 as my single novel Haplogroup, hopefully officially moving to the ISOGG Public status.

I am working with other FGC kits to narrow down which new SNPs should be further tested. So keep them coming to me.

MJost

MacUalraig
12-11-2013, 05:36 PM
Is anyone doing any analysis of their lower quality (**/***) calls or even testing them to see how reliable they are? I have been looking at some that give me conflicting phylogenies. This is not surprising I guess so it may be a sign I should just ignore them, but one had potential and might be worth testing.

MacUalraig

LarryWalker
12-11-2013, 08:45 PM
Is anyone doing any analysis of their lower quality (**/***) calls or even testing them to see how reliable they are? I have been looking at some that give me conflicting phylogenies. This is not surprising I guess so it may be a sign I should just ignore them, but one had potential and might be worth testing.

MacUalraig

My "terminal" SNP through FTDNA testing had long been DF41+, so I was surprised when it showed up with ** on my variant compare report. Gregory Magoon responded to that observation with the following:


Regarding DF41 being classified as **, first I should give some background (which you may already be aware of):
There are essentially two different types of bioinformatic analysis that are traditionally used to interpret next-gen sequencing results. The first, which might be called "genotyping", involves looking at sites of known variation (e.g. DF41) and figuring out what is the allele at that site; this is what is done by the gtype report. The second goes by the name of "variant discovery", "variant identification", or "variant calling" ("variant" may be also replaced by "SNP" to refer to that particular type of variant which is most commonly discussed); here, the idea is to identify differences from the reference human genome without any a priori knowledge about what these variations are or where they will be found (though often the variants that are found may be identified as corresponding to known variants after the fact); this process is the basis for the "variantCompare" and "haplogroupCompare" reports.

With that as background, the underlying details of how the reliability flag is determined in the variantCompare (and haplogroupCompare) report are considered proprietary to FGC, but I can comment that the goal here is to avoid the identification of significant numbers of spurious, false-positive variants, as next-gen sequencing methods are prone to doing. Certain regions of chrY are more prone to these issues than others. The reliability indicator indicates the likelihood of a genuine variant for purposes of novel variant identification (rather than probability of a particular genotype). So, certain well-known variants may be classified as ** or *** when in fact underlying results are solid (and further details can be seen on the gtype report). The reliability flag is more useful for variants that have not been extensively studied (e.g. confirmed by conventional sequencing). We will try to make these subtleties clearer in future versions of the report.

MacUalraig
12-11-2013, 09:58 PM
My "terminal" SNP through FTDNA testing had long been DF41+, so I was surprised when it showed up with ** on my variant compare report. Gregory Magoon responded to that observation with the following:

Larry, thanks, that was most interesting although a bit tricky to apply to my case which involves two shared INDELS. One was unnamed and one was a Z class but I suspect both fall into the 'untested' category. I might run it past Greg for further comment. At the moment I find analysing all this stuff such fun I keep wanting to run confirmatory tests on everything. :)

MJost
12-12-2013, 03:48 PM
For the 304 private SNP's and InDel's mutations I have under DF13, using 4000 or either 6000 YBP for the age of L21 (as

DF13 is very close to the age of L21) and 30 years per generation, there is 133.33 generations back to L21 which

equates to 304/133.33 = 2.28 mutations/gen and at a TMRCA of 6k ybp there are 304/200 = 1.52 mutations/gen.

My SNPs listed are from subclade - R1 and below. (Matches: M173+, S1+, P225+, P231+, P233+, P234+, P236+, P238+) or

M173+ (also known as P241, Page29, PF6126, PAGES00029).

I have a total number of 1,495 private and public mutations under R1, using 2.28 mutations per generation, would need

655.7 generations or 19,671 years to occur. The 1,495 SNPs using the 1.52 (at a 6k L21 age) factor equates to 983.6

generations or 28,158 years.

T. Karafet et al. estimated the age of R1, the parent of R1b, as 18,500 years before present.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336805/

MJost

palamede
12-12-2013, 05:34 PM
My public SNPs shared with reference samples (1036 total variants)
INDELs shared with reference samples (155 total variants)
1,191 total shared with reference samples

What is the first ancestor taken by FGC for 1191 total shared : A0 ? A1 ? B ? CT ? F ? K ? P ? R ?



Any qualifications to these numbers?

Then you change your mode of calculation.
What does this mean ?





For mutations I have under DF13, using 4000 or 6000 YBP for the age of L21 (as DF13 is very close to the age of L21) and 30 years per generation, there are 0.44 to 0.65 mutations respectively that occur each generation.


I am not a good computer but 4000 years=133,33 gen and 6000 years=200 gen
Therefore for 304 mutations we have 304/133,33=2,28 mutations/gen and 304/200=1,52mutations/gen

Where am I wrong ?

George Chandler
12-12-2013, 09:23 PM
It's my belief that it's a combination of L21 being older than thought and kinks being worked out in terms of the testing process (still think it's the best way to go). It will be interesting to see if I match any of your SNP's. Probably a good plan wait for confirmation before posting the results publicly.

George

Mikewww
12-13-2013, 04:40 PM
You and everybody else have my permission......... The more public the better as DNA data that is not widely shared is next to worthless even to its owner.

Agreed. To that end, I've tried to set up a mechanism that everyone in the L21 project will be able to see prospective SNPs that they might consider testing for. The FGC identified SNPs could be very important to a lot of people, but they need to know about them and need to have some kind of idea where an SNP is positioned and what kinds of Y STR haplotypes seem to be derived for it.

I have now created a system to gather and consolidate derived SNP results from FGC, Chromo 2 and FTDNA public project reports. This is the spreadsheet I'm using.
https://dl.dropboxusercontent.com/u/17907527/R1b-L21_SNPs.zip

This weekend I'll work on integrating the haplogroup labeling and SNP results into the large R1b-L21_Haplotypes spreadsheets with all of the variety assignments, etc. Folks like Alex W use that for various analysis.

In the R1b-L21_SNPs spreadsheet above I have a tab/worksheet for FGC relevant SNP results. I'd like to make sure to get the high quality potentially public SNPs downstream of L21 on this list. Here is a screen shot of the "FGCin" tab.
https://dl.dropboxusercontent.com/u/17907527/R1b-L21_in_SNPs_FGCin.pdf

On the "SNPindex" tab, I've added the following. I don't want to go overboard on speculation, but what I else do I need to add?
FGC5496 R1b-L21>DF13>FGC5496+
FGC3218 approx. equiv. to L21
FGC164 approx. equiv. to DF13

Once I can incorporate the FGC "tree" SNPs, they'll affect, to the extent we know, the L21 phylogeny, the haplogroup labels, variety assignments and "Relevant SNP" results on the R1b-L21_Haplotypes spreadsheet.

I'm supportive of any systems you want to use, but if you need a place for people to "opt in" to sharing, just instruct them upload their files to file folder in the R1b-L21-Project yahoo group I've set up, similar to like what we've done for Chromo 2 "raw" results. We just need to have a consistent file naming format. I advocate the spreadsheet ID (which is just "f" and the kit #), an underscore, the surname, an underscore and then "FGC". For example ("f148326_Jost_FGC_Summary.xlsx").
http://groups.yahoo.com/neo/groups/R1b-L21-Project/files/FGC_L21_results/
Any one who has uploaded or sent something to me to upload has effectively opted in to sharing.

Yahoo group is quirky. If you want me to upload a file, just email it to me.
1060
(I'm trying to learn a lesson from Robert so the .png file has my email. :) )

MitchellSince1893
12-13-2013, 05:47 PM
Isn't 2.28 or 1.5 mutations per generation much higher than expected?

I thought I read a study that observed 1 mutation every 3 generations I.e 1 every ~90 years.

Maybe that was referring to STR mutations?

Confused.

razyn
12-13-2013, 06:13 PM
When trying to correlate a number of mutations with a number of generations, isn't there an issue with the observed (though perhaps not rigorously tested) phenomenon of handfuls of SNP mutations occurring at the same time, though in different loci? That would be those groups observable e.g. on the ISOGG tree, or Chris Morley's experimental Geno2-based tree, wherein a good many SNPs are "on the same level."

MJost
12-13-2013, 06:26 PM
I am not a good computer but 4000 years=133,33 gen and 6000 years=200 gen
Therefore for 304 mutations we have 304/133,33=2,28 mutations/gen and 304/200=1,52mutations/gen

Where am I wrong ?

No you correct, I was wrong. I completely re-did my above post. Thx for pointing it out. I have no clue how I got that answer I previously posted but its been corrected.

MJost

Muircheartaigh
12-13-2013, 06:38 PM
In the R1b-L21_SNPs spreadsheet above I have a tab/worksheet for FGC relevant SNP results. I'd like to make sure to get the high quality potentially public SNPs downstream of L21 on this list. Here is a screen shot of the "FGCin" tab.
https://dl.dropboxusercontent.com/u/17907527/R1b-L21_in_SNPs_FGCin.pdf

Mike, your spreadsheet shows me as Z253>PF825. I think this should be McClure. According to results from members of my cluster 253-1711-16 I am almost certainly negative for PF825.

Ray Murta f205635

George Chandler
12-13-2013, 06:39 PM
No you correct, I was wrong. I completely re-did my above post. Thx for pointing it out. I have no clue how I got that answer I previously posted but its been corrected.

MJost

Mark,
You still have 64 private high quality SNP's above 95% which should give a possible age of 5,700 years for DF13. How many other SNP's are between your 64 private and DF13? I'm trying to get the 2 other Chandler branches to test FGC as our MRCA is 12 generations to see if the 1 mutation per 3 generations will hold up.

George

MJost
12-13-2013, 06:54 PM
Isn't 2.28 or 1.5 mutations per generation much higher than expected?

I thought I read a study that observed 1 mutation every 3 generations I.e 1 every ~90 years.

Maybe that was referring to STR mutations?

Confused.

I have seen the 1 mutation per '90' year number else where too. But what I did was to assume what the age of L21 either a 4K or 6K TMRCA. I am seeing L21 at around 3.8K ybp in my use of over 9K haplotypes to calculate a TMRCA. So looking at the number of my discovered SNPs and INDel's mutations under L21(DF13) and calibrated the mutation per generation to both 4k and 6K ages. Then extrapolating it using all of my mutations under R1 using my calibrated rate of 2.28 or 1.5 rate to calculate how many years it would take to produce that many mutations. It was just a quick and dirty calculation. My point of all of this was that it was to show that my number of BP mutations appear to be very close to the age that Karafet calculated for R1. Knowing this 2.28 mutation rate will allow age calculations between subclades of the FGC BP data. This will get real interesting to see those kind of results that may break or confirm existing knowledge.

MJost

George Chandler
12-13-2013, 06:54 PM
Isn't 2.28 or 1.5 mutations per generation much higher than expected?

I thought I read a study that observed 1 mutation every 3 generations I.e 1 every ~90 years.

Maybe that was referring to STR mutations?

Confused.

No the possible mutation rate thrown around is 1 per 3 generations for SNP's discovered through FG testing. The statistical mutation rate for STR's vary for each one.

George

MJost
12-13-2013, 07:35 PM
Mark,
You still have 64 private high quality SNP's above 95% which should give a possible age of 5,700 years for DF13. How many other SNP's are between your 64 private and DF13? I'm trying to get the 2 other Chandler branches to test FGC as our MRCA is 12 generations to see if the 1 mutation per 3 generations will hold up.

George
One would have to recalibrate the mutation rate but I don't know how that would be done since the ancestral count above L21 would be oranges and the derived new HQ SNPs would be Apples.


MJost

George Chandler
12-13-2013, 07:59 PM
One would have to recalibrate the mutation rate but I don't know how that would be done since the ancestral count above L21 would be oranges and the derived new HQ SNPs would be Apples.


MJost

Even though I believe L21 is older than the analysis shows I would still use the STR age estimates until something can be proven with the 1 per 3 generation for SNP's discovered using FG testing. It would be interesting to see what you get mixing the 2 processes but I'm not sure how scientific that would be in terms of getting a more reliable age estimate (if I understood you correctly).

George

Mikewww
12-13-2013, 08:02 PM
Mike, your spreadsheet shows me as Z253>PF825. I think this should be McClure. According to results from members of my cluster 253-1711-16 I am almost certainly negative for PF825.

Ray Murta f205635

Got it, Ray. Thanks for checking. The BISin and FGCin spreadsheets are manually entered, hence my screw-up. I can copy/paste but my typing stinks. My mind goes at a different speed than my fingers. It'll be fixed before the end of the day on-line (in the yahoo group.)

EDIT: There may be one other thing. PF825 in Chromo 2 is showing a lot of false positives, apparently.

Mikewww
12-13-2013, 08:03 PM
One would have to recalibrate the mutation rate but I don't know how that would be done since the ancestral count above L21 would be oranges and the derived new HQ SNPs would be Apples.


MJost

I would suggest having someone like Greg Magoon or Ken Nordtvedt give you an estimated mutation rate. The rate has to based on the coverage of the FGC tests.

Muircheartaigh
12-13-2013, 08:52 PM
I would suggest having someone like Greg Magoon or Ken Nordtvedt give you an estimated mutation rate. The rate has to based on the coverage of the FGC tests.

We will soon have results from FGC of around 25 R-L21 candidates which will enable us to make a reasonable estimate of the average number of SNPs per member below R-L21. This information on its own will not enable us to determine SNP mutation rate or the age of R-L21.

However there are currently over 200 tests in progress with FGC so R-L21 is only about 10% of the total being tested so there will presumably be good cover across many major haplogroups which will enable us to determine, by triangulation, the number of SNPs that have occurred since branching of the major Haplogroups. If we have a rough estimation of the ages of some of the branching of major haplogroups we can make an estimate of the mutation rates and by interpolation can determine with reasonable accuracy, the age of recent SNPs.

Ray

Rory Cain
12-14-2013, 04:19 AM
The R-DF63 men HG02014 and HG00243 are also positive for FGC3218, so this SNP can't be any lower down than L21. As I mentioned above, I also don't see any men outside of R-L21 listed as positive for this SNP on my report, so I do think it is likely equivalent to L21. If PGP40 is negative for this SNP, perhaps it's an error, or perhaps it a back mutation.

Alex

Thanks Alex. May I seek your advice on FGC5790 which is supposedly a new and private InDel found in my sample. Strange thing is that it already has another ID, namely rs34112170. Many of the FGC series that you, David and I share have an "rs" ID already, so I tend to take such an ID as indicating that FGC5790/rs34112170 may have been observed before. But unlike the SNPs and InDels you, David & I share, and which have alongside them the kit numbers of those samples in which they were previously found, there is no kit number to indicate who else in the world has FGC5790/34112170. I would have to assume that Fullgenomes Corp didn't know either as it would be a strange omission. Any ideas?

Rory

jdean
12-14-2013, 11:15 AM
I would suggest having someone like Greg Magoon or Ken Nordtvedt give you an estimated mutation rate. The rate has to based on the coverage of the FGC tests.

Ray Banks has just posted this quite lengthy 'article' regarding the SNP mutation rate on Facebook, he appears to be coming out in favour of 1 SNP per 200 yrs !!

https://www.facebook.com/groups/isogg/permalink/10152097130632922/

New genetic findings regarding the 5300-year-old Iceman mummy, Oetzi.

Studies earlier this year supplied data suggesting two different calculations for how many years are represented by each SNP mutation in the higher quality, mappable areas of Y-DNA. I have come across new data that takes sides with one of the two studies. Oetzi the Iceman is perhaps the best test for checking the validity of the proposed dating because he is reliably dated to 5300 yrs by carbon dating and was the only ancient person ever to have full Y sequencing.

Francalacci in a sequencing study of Sardinia suggested that a SNP mutation in the described chromsome area occurs every 205 yrs +/- 50 yrs. Poznik in a study of a much smaller number, but more geographically diverse, men did not state such a figure for his men, but it can be deduced it was probably half the number. Francalacci calibrated his calculations to the first settlements in Sardinia, and Poznik to the first peopling of the Americas.

Oetzi was reported in a study as belonging to the G-L91 subgroup. But the raw data available in his public data file (BAM file) indicates he is positive more specifically for the G-L166 mutation which characterizes L91’s subgroup.

We received this week high-coverage (50x) YDNA sequencing of the sample of the man of German ancestry in whom L166 was first discovered. This was ordered through Full Genomes Corp. There are other L166 sequenced samples available for comparison, both Asian and European, and – of course – Oetzi’s.

Oetzi’s sample is not perfect, and that problem makes it difficult to put together a study involving my findings for publication. The sample is also unfortunately in the old Build36 version of the chromosome location mapping, and that makes it difficult to simultaneously compare with all the other samples, a process which can improve the quality of reads for him and possibly bring out some additional positive results. There are about 600 or so known shared G SNPs earlier than the L166 subgroup which Oetzi would be expected to share, but he has an unusual number of “no reads” comparatively. Oetzi was sequenced with low-coverage sequencing, but others with similar sequencing had fewer no reads for expected mutations.

In this context, the newly sequenced L166 has 36 quality SNPs unreported in other L166 men. He is the closest man so far to Oetzi, sharing with him the only L166 SNP negative in the Asian L166. There may be about 10 L166+ men in the Francalacci data. L166 results were not reported for them, but their status can be inferred by the constant sharing of SNPs with proven L166 men. These 10 were not reported also for FGC5672 which is negative in the Asian contingent and present in the men just tested and in Oetzi.

So multiplying the 36 SNPs from the newly tested man that are unique to him by the 200 yrs suggested by Francalacci, we come up with 7200 yrs to the nearest shared common ancestor, which would be Oetzi. Poznik, on the other hand, would indicate this calculates to about 3600 yrs. The latter clearly cannot be the case because Oetzi is 5300 yrs old.

Oetzi could share a few more SNPs with the newly tested man which could not be read. That would reduce Francalacci’s time calculation to perhaps 6800-7000 yrs ago to the shared male ancestor with Oetzi and change Poznik’s to perhaps 3300 to 1500 yrs ago. This makes Poznik’s time calculation less tenable.

All this just suggests that the 200 yrs per SNP listed in Francalacci is the most valid. Without more good reads and higher coverage sequencing of Oetzi, my observations do not prove anything, just suggest it.

In our prepublication paper involving 1000 Genomes Project samples and a few other samples,
http://biorxiv.org/content/early/2013/11/24/000802.full-text.pdf+html
we point out that the Amazonian Indian sample has an unusually large number of these unshared (singleton) SNPs. This might indicate some branches of Ameridians have ancestors that predate the peopling of the Americas. Poznik wrote: “Because the M3 mutation appears to be specific to the Americas (20), it likely occurred after the initial entry.” He used only two Maya Indian samples to make this calculation. If the M3 divergence occurred earlier, Poznik would have to reset his yrs/SNP calculation closer to Francalacci’s.

Francalacci’s dating at 200 yrs/SNP would place the emergence of the G branch from F (the first divergence within the G to T haplogroups) at perhaps 100,000 yrs ago. Various researchers initially were listing the age of G’s divergence at abt 21,000 yrs ago based on the formula they use as applied to the number of STR marker mutations, and a calculation in the earlier study (in sync with Poznik) suggested the divergence of the G through T haplogroups from F took place about 50,000 yrs ago.

I personally have noted some inconsistencies in the number of SNPs per haplogroup in the 1000 Genomes data. This has not been fully explored. At times these haplogroups were apparently nothing more than a small family group existing for millennia. Perhaps longer haplogroup-specific longevity of males or a culture that allowed older men to have more wives might be involved. Or one haplogroup’s ancestors camped on a uranium deposit? So this time calculation does not seem a simple problem to me.

Ray Banks

warwick
12-14-2013, 04:50 PM
There's a lot of strong research in other papers that the rate is 1/75-90 years. We should be careful about this question, particularly since in most other data the 200 year figure is not very plausible.

George Chandler
12-14-2013, 05:31 PM
There's a lot of strong research in other papers that the rate is 1/75-90 years. We should be careful about this question, particularly since in most other data the 200 year figure is not very plausible.

Would the difference partly be a result of what they consider high quality SNP's?

George

David Wilson
12-14-2013, 09:54 PM
Sad news to report: I got a message from FGC today that my UCLA beta test results failed QC. They'll be starting me over with another sample collection kit.

Rory Cain
12-14-2013, 10:16 PM
Thanks Alex. May I seek your advice on FGC5790 which is supposedly a new and private InDel found in my sample. Strange thing is that it already has another ID, namely rs34112170.
Rory

Never mind, I found a reference to rs34112170 and it looks like FGC gave me a bum steer if they think FGC5790 equals rs34112170. FGC5790 TA>T (deletion) is at b37 position 5252635 while rs34112170 -/A (insertion) is at NCB position 91301272. No correlation between these two InDels as far as I can see.

Looks like I can consign rs34112170 to the trash can along with V161.1+, V190+, F1345+, M118+, M236+, P92+, P80+, Z346+, IMS-JST029149+, CTS616+, IMS-JST022457+, P266+ & V203+. To be positive for SNPs from such a weird collection of haplogroups would have been amazing. These false positives may well have occurred in other kits too so beware.

hoxgi
12-15-2013, 01:26 AM
McClure PF825+ (from his Geno 2.0 results) shares two high quality SNPs (FGC3268 and FGC3220) from his FG results with one reference kit kit from the 1000 Genomes Project, HG01136, which is Z253+. Neither of these SNPs are positive in any of the other references used by FG, including several more Z253+ kits and three Z2534+ kits.

Before PF825 was discovered under Z253, McClure's STR grouping was one of the 253-1716 varieties in Mike's spreadsheet. There are a number of other 253-1716 varieties in which a downstream SNP has not been detected. Either or both of FGC3268 and FGC3220 could turn out to be very useful in defining this grouping or one or more of its subdivisions. Ray Murta's FG results could be very informative as he belongs to one of the 253-1716 varieties.

PF825 is proving difficult to reconcile across the different testing companies. According to FTDNA, PF825.1 is in Haplogroup A and PF825.2 is under Z253. The ISOGG SNP index has PF825.1 as investigational in Haplogroup A, and PF825.2 as defining R1b1a2a1a2c1f3 (below Z253), but both supposedly have the same mutation G>A.

Chromo 2.0 reports everyone in Haplogroup R as being PF825+ (with G being the derived form), referring to PF825.1 above, and has stated that the PF825 under Z253 in McClure's grouping (PF825.2) is actually a back-mutation (so derived G back to ancestral A).

PF825 was not listed in McClure's FG results, or so I thought. However, searching for the b37 designation for PF825 (17054132), I found it was designated as M9194-, with McClure's result being + and all the reference kits -. Presumably the minus in the SNP's name means that the ancestral form, the back-mutation, was being tested, and McClure's + result indicates that he does have the back-mutation and all the reference kits do not.

So, if I've interpreted this correctly, HG01136 does not have McClure's PF825 back-mutation, which increases the likelihood that the two SNPs they share, FGC3268 and FGC3220, will be helpful in breaking down the 253-1716 varieties.

Greg H

Williamson
12-16-2013, 01:56 AM
Never mind, I found a reference to rs34112170 and it looks like FGC gave me a bum steer if they think FGC5790 equals rs34112170. FGC5790 TA>T (deletion) is at b37 position 5252635 while rs34112170 -/A (insertion) is at NCB position 91301272. No correlation between these two InDels as far as I can see.

Looks like I can consign rs34112170 to the trash can along with V161.1+, V190+, F1345+, M118+, M236+, P92+, P80+, Z346+, IMS-JST029149+, CTS616+, IMS-JST022457+, P266+ & V203+. To be positive for SNPs from such a weird collection of haplogroups would have been amazing. These false positives may well have occurred in other kits too so beware.

Hi Rory,

I found rs34112170 on the NCBI website,

http://www.ncbi.nlm.nih.gov/snp/?term=rs34112170

It looks like FGC got it right, the b37 position is 5252635. To me, this looks like one of those funny situations which looks more like an STR than a just a random INDEL. There are 11 'A's in a row starting at 5252636 in the reference sequence, you have only 10. I don't know why the entry was added to the database.

Alex

Rory Cain
12-16-2013, 04:00 AM
Hi Rory,

I found rs34112170 on the NCBI website,

http://www.ncbi.nlm.nih.gov/snp/?term=rs34112170

It looks like FGC got it right, the b37 position is 5252635. To me, this looks like one of those funny situations which looks more like an STR than a just a random INDEL. There are 11 'A's in a row starting at 5252636 in the reference sequence, you have only 10. I don't know why the entry was added to the database.

Alex

OK, apologies to FGC if they in fact got it right in identifying FGC5790 with rs34112170. I guess I am now to assume that my deletion was not the first occurrence and that somebody (despite his lack of a kit number or other ID?) was the first occurrence. How mysterious.

I observe a degree of disinterest in InDels amongst DNA researchers, and assume InDels are more "flighty" than SNPs, thus less to be relied upon. However as this is the only one amongst my 36 new SNPs and 8 new InDels to already have an "rs" number and thus a previous occurrence, maybe it would be worth following up with further testing. Unfortunately though, with no kit number or other ID, we cannot even confirm if the mystery rs34112170+ was even the same haplogroup as myself. Just looking for a way forward with at least one of the new polymrphisms.

Williamson
12-16-2013, 05:36 AM
I observe a degree of disinterest in InDels amongst DNA researchers, and assume InDels are more "flighty" than SNPs, thus less to be relied upon. However as this is the only one amongst my 36 new SNPs and 8 new InDels to already have an "rs" number and thus a previous occurrence, maybe it would be worth following up with further testing. Unfortunately though, with no kit number or other ID, we cannot even confirm if the mystery rs34112170+ was even the same haplogroup as myself. Just looking for a way forward with at least one of the new polymrphisms.

I understand your desire for progress. I feel the same way. We've spent a lot of money for these tests, and we want tangible results. There are others taking FullGenomes tests, Big Y tests, and so on. Those will all yield more results we can compare to. I'm confident progress will take place.

With regard to rs34112170, it may be that someone more experienced than I could find out some more information. My thought is that it may just be a less stable position, more prone to mutation.

I have 3 INDELs given FGC numbers from my DNA. One is shared with NA12043 (also Little Scottish Cluster) and the other 2 are "Private". At least one of the INDELs, FGC3217 is most definitely "flighty". It is a deletion at position 21464771 from GTTC to G. I've looked at the sequence around the deletion and it looks to be an STR, although I don't know if it has a name or not. The reference sequence has 16 repeats of [TTC] starting at 21464772. Because of my deletion, I have only 15 repeats. When I checked the sequence for NA12043, I noticed he has only 14 repeats. McClure, discussed above, has the FGC3217 mutation as well, even though he is R-Z253 and I'm R-DF21. I think you might even have 17 repeats Rory, because of the *** G -> GTTC insertion you have at the "site of FGC3217". At least for the time being, we may have to take some INDELs as being much less stable than others.

I think this is going to be a learning process for all of us. Playing around with my own results, I now have a much better understanding as to why SNP identification is not always straight forward. I think FGC has done a fantastic job so far at identifying so many potential SNPs and INDELs, and I do expect them to do more in the future. In the mean time, we have been left on our own to make connections and discoveries. Although it's nice when we're handed a complete analysis, I often enjoy doing the work as well.

Alex

MacUalraig
12-16-2013, 08:55 AM
OK, apologies to FGC if they in fact got it right in identifying FGC5790 with rs34112170. I guess I am now to assume that my deletion was not the first occurrence and that somebody (despite his lack of a kit number or other ID?) was the first occurrence. How mysterious.

I observe a degree of disinterest in InDels amongst DNA researchers, and assume InDels are more "flighty" than SNPs, thus less to be relied upon. However as this is the only one amongst my 36 new SNPs and 8 new InDels to already have an "rs" number and thus a previous occurrence, maybe it would be worth following up with further testing. Unfortunately though, with no kit number or other ID, we cannot even confirm if the mystery rs34112170+ was even the same haplogroup as myself. Just looking for a way forward with at least one of the new polymrphisms.

I have analysed my INDELs with the expert help of Thomas Krahn, some of mine he deemed to be STR-like but still potentially useful. I didn't get that many high quality ones though.

George Chandler
12-16-2013, 04:52 PM
It is a deletion at position 21464771 from GTTC to G.

Alex

Hi Alex,
I'm not sure..maybe I've missed something here that Justin can correct me on. The SNP "change" being a mutation in the base pair at a specific location (ie the Ancestral T changing to C) and the "deletion" is the loss of a base instead of the mutation at a specific loaction. Maybe I've missed something in your message?

Thanks
George

Williamson
12-17-2013, 05:15 AM
Hi Alex,
I'm not sure..maybe I've missed something here that Justin can correct me on. The SNP "change" being a mutation in the base pair at a specific location (ie the Ancestral T changing to C) and the "deletion" is the loss of a base instead of the mutation at a specific loaction. Maybe I've missed something in your message?


Hi George,

It's a deletion of 3 base pairs. The TTC following the G at position 21464771 are deleted.

That is also why it looks like an STR mutation. Starting at position 21464772, immediately after the G, the ancestral DNA sequence has 16 copies of TTC. Because of the 3 base pair deletion, my DNA has only 15 copies of TTC following the G.

Alex

Mikewww
12-17-2013, 03:02 PM
Alex, do I understand this correctly?

P9UH4A Williamson has the following very reliable (no warnings) newly discovered SNPs in common with NA12043 (R-DF21) but not with others (so far) under L21:

FGC3177+
FGC3183+
FGC3184+
FGC3187+
FGC3188+
FGC3207+
FGC3189+
FGC3209+
FGC3190+
FGC3210+

P9UH4A has these derived and NA12043 is ancestral, in fact, so far they are unique to P9UH4A:

FGC3204+
FGC3206+
FGC3211+
FGC3214+

P9UH4A has these derived while and NA12043 is a no call and everyone else tested under L21, is ancestral:

FGC3205+
FGC3208+
FGC3212+

Are any of these identical (synonyms for) with S190, S424 or S426?

P.S. - on the SNPindex table I use for L21 spreadsheet haplogroup labeling I use initials to describe the source so I have ARW, DFR, JFW, etc. That's what those abbreviations are.

Mikewww
12-17-2013, 03:17 PM
Here is another. If I understand it, MRD4PA Trainor and HG02501 (R-Z2961) are both derived for but none of the other L21 FGC or academic project folks are:

FGC6540+
FGC6564+

MRD4PA is derived/positive for these while HG02501 is ancestral for these:

FGC6547+
FGC6548+
FGC6549+
FGC6550+
FGC6559+
FGC6560+
FGC6561+
FGC6562+
FGC6563+
FGC6565+
FGC6567+
FGC6568+
FGC6570+
FGC6571+
FGC6572+
FGC6541+
FGC6574+
FGC6575+
FGC6576+
FGC6577+
FGC6579+
FGC6580+
FGC6581+
FGC6583+
FGC6584+
FGC6585+

MRD4PA is positive but we don't know the status for HG02501:

FGC6573+
FGC6582+

MRD4PA should be positive for S476 since J.F. Wilson has it upstream of DF23/S193 but downstream of D49/S474 Do we know if either FGC6540 or FGC6564 are identical (a synonym for) S476?

Williamson
12-17-2013, 08:00 PM
Well done Mike! Many of them have S-names. I've included the S-names in red in the quoted text below. I've also added one additional SNP, CTS9333, to your list below in blue. It already had a CTS name and so wasn't given an FGC name. It is another very reliable SNP that is common to just NA12043 and myself.


P9UH4A Williamson has the following very reliable (no warnings) newly discovered SNPs in common with NA12043 (R-DF21) but not with others (so far) under L21:

FGC3177+ (S3028)
FGC3183+
FGC3184+ (S3032)
FGC3187+ (S3057)
FGC3188+ (S3058)
FGC3207+ (S423)
FGC3189+ (S424)
FGC3209+
FGC3190+ (S426)
FGC3210+
CTS9333+ (S307)

P9UH4A has these derived and NA12043 is ancestral, in fact, so far they are unique to P9UH4A:

FGC3204+
FGC3206+
FGC3211+
FGC3214+

P9UH4A has these derived while and NA12043 is a no call and everyone else tested under L21, is ancestral:

FGC3205+
FGC3208+ (S301)
FGC3212+




Are any of these identical (synonyms for) with S190, S424 or S426?
S190/CTS2187 is a * result for me, and so is not included in the above list. S424 and S426 are in the list above.

Regards,
Alex

Mikewww
12-18-2013, 05:17 PM
Here is my attempt at understanding 0FW1RA Jost/Watterson's very reliable (no warnings) newly discovered SNPs in common with PGP50 (R-DF13) but not with others (so far) under L21:

FGC5496+

0FW1RA also has this SNP and it is equivalent to S but may be unreliable.

FGC5495+

0FW1RA is derived for these, but PGP50 is ancestral:

FGC5507+
FGC5508+
FGC5509+
FGC5516+
FGC5517+
FGC5518+
FGC5519+
FGC5520+
FGC5521+
FGC5522+
FGC5523+
FGC5524+
FGC5525+
FGC5526+
FGC5527+
FGC5528+
FGC5493+
FGC5529+
FGC5530+
FGC5531+
FGC5532+
FGC5533+
FGC5534+
FGC5535+
FGC5536+
FGC5537+
FGC5538+
FGC5539+
FGC5540+
FGC5541+
FGC5542+
FGC5543+
FGC5544+
FGC5550+
FGC5551+
FGC5552+
FGC5553+
FGC5554+
FGC5555+
FGC5556+
FGC5560+
PF432+
Z3872+

What's the status of PF432 and Z3872? They must have been found elsewhere. Are they recurrent?

Mikewww
12-18-2013, 05:20 PM
Well done Mike! Many of them have S-names. I've included the S-names in red in the quoted text below. I've also added one additional SNP, CTS9333, to your list below in blue. It already had a CTS name and so wasn't given an FGC name. It is another very reliable SNP that is common to just NA12043 and myself.

S190/CTS2187 is a * result for me, and so is not included in the above list. S424 and S426 are in the list above ...

Thanks for updating me on the S series labels. I'm assuming all of those you listed besides an FGC series label are identical (synonyms). Correct?

I've now included those you've pointed out in my spreadsheet conversion table so when we can get more people to upload their raw Chromo 2 results we'll see what we pick up.

MJost
12-18-2013, 10:14 PM
Here is my attempt at understanding 0FW1RA Jost/Watterson's very reliable (no warnings) newly discovered SNPs in common with PGP50 (R-DF13) but not with others (so far) under L21:

FGC5496+



What's the status of PF432 and Z3872? They must have been found elsewhere. Are they recurrent?
Mike,

I have already checked into these,

PF432 was also found in FG1012A-S116-Hatton,

Z3872 has an X-Cross over: X + 89161266 89161765

So there was no pudding there. But good Eye.

MJost

Williamson
12-19-2013, 02:07 AM
I'm assuming all of those you listed besides an FGC series label are identical (synonyms). Correct?
Yes, that is correct. The S-numbers following each SNP are just a different name for the exact same SNP at the exact same position.

Alex

Celtarion
01-08-2014, 11:59 PM
It seems that FGC might have received batch 5 back and it may be under quality assessment... Someone in the U106 group got an email stating that his sample is not good quality. Anyone got any news about batch 5? Last Justin's post was saying final result 20/01.

"Woohoo! After two months waiting to get into batch 5 from early October, my sample's not good quality, so I'll have to start over with a different sample kit. But the SNP tsunami will not be as big, so there's that."

Dubhthach
01-09-2014, 09:28 AM
I'm in Batch 5 and haven't received any email regarding my own sample, however the "anonymous DF41" (1426) did receive an email stating that his sample didn't contain enough high quality DNA and that they were sending him a new kit.

-Paul
(DF41+)

Celtarion
01-09-2014, 03:02 PM
I haven't received any email either, so wait and see, final approach in few days...!

Joss.

kenmunn
01-09-2014, 03:58 PM
Another Batch #5 sample also did not contain high enough quality DNA for test. New sample collection kit due in today.
Godwin (Z251+)

Mikewww
01-09-2014, 04:18 PM
Has f228772 Reid 513- uas 's FGC results come in yet?

seferhabahir
01-10-2014, 07:42 AM
Another Batch #5 sample also did not contain high enough quality DNA for test. New sample collection kit due in today.
Godwin (Z251+)

Big bummer for Z251+ fans (like me). I have not received an email about my kit. Maybe emails are going out sequentially after various kits fail quality control. I hope I don't get one.

Mikewww
01-24-2014, 04:26 PM
Has f228772 Reid 513- uas 's FGC results come in yet?

Sorry to be repetitive. Do we know anything about the L513+ Reid's results?

Mikewww
01-30-2014, 03:15 PM
Any M222+ FGC results that have come in yet? I'm aware there is a Kennedy but I don't know if he will post his variant comparison report. Are there any others?

LarryWalker
01-30-2014, 09:43 PM
Folks,
I just checked the YFull.com tree at http://www.yfull.com/tree/R/ and it appears that I am the only L21+ who has posted his results to YFull (kit YF01387). I encourage other L21's with results to also post theirs to YFull. It is presently free and has some nice tools.

Mikewww
02-04-2014, 02:21 PM
People who want to do one at a time SNP testing that FGC customers or Chromo 2 customers (or anyone for that matter) may want to use YSEQ. If you are a YSEQ customer and you are L21+ or derived for some downstream subclade of L21 please post your YSEQ ID # and corresponding FTDNA kit or Ysearch ID (if you have those).

It's important to also join the public browser group for R1b-L21, ID=11.
http://shop.yseq.net/group_alleles.php?gid=11

Thomas Krahn was kind of enough to set this up for us. Mark J was kind enough to do the administrative duties to make this work.

I'm keeping a cross-reference so that I can copy the SNP results into the large R1b-L21_Haplotypes spreadsheet so the haplogroup assignments will be correct and more people will be encouraged to intelligent plan SNP testing (of these new SNPs) if that is what they want. I automatically copy the Y DNA SNP report from the FTDNA R-L21plus and M222 (R1b1c7) projects about once a week. This puts Krahn's YSEQ SNPs on par with FTDNA's for ease of reporting/sharing...

but only if you join the right public browser group and you post your YSEQ ID and FTDNA kit # so I can complete the cross-reference table.

RobertCasey
02-04-2014, 10:16 PM
... but only if you join the right public browser group and you post your YSEQ ID and FTDNA kit # so I can complete the cross-reference table.

I had my L226 tester join the L21 project in YSEQ. He is YSEQ Customer #62 and FTDNA ID 131349.

FGC498 is G- (which I assume to be A+) - My FGC498 is G to A (or A+) - so we are both positive. This YSNP remains between our common ancestor under L226 and below Z253.
I later discovered that the other positive test for FGC498 is not R1b, so this YSNP has at least two mutations - probably not a good YSNP to test in the future.

FGC5626 - we are both T+ - again no difference indicating this YSNP remains between our common ancestor under L226 and below Z253. - so no new discoveries for the first two results.

Keeping my fingers crossed that one of the last two come in negative - creating a new ISOGG branch under L226. We only share one off modal marker between these two clusters under L226
and have a GD much larger than 7 at 67 markers. My Casey belongs to the South Carolina cluster and 131349 belongs to the Munster Cluster (even though he has a proven ancestor in
South Carolina which is the only South Carolina submission to belong to Munster cluster).

Here is the procedure required:

1) Have your tester log onto his YSEQ account via his email and YSEQ account password.
2) It will tell you that your Customer Number after you log in. You should make sure that your YSEQ # and FTDNA # gets posted to let Mike W track the results.
3) Click the "My Account" button in the top right corner of the screen.
4) Click the Group Browser link.
5) Select Group 11 (R1b-L21 project) and click the Join button at the bottom portion of the screen (in the middle).

You are done.

LarryWalker
02-07-2014, 12:40 AM
YFull Public Groups have now been set up for L21 and DF41 at http://www.yfull.com/groups/ . This is where we are going to be able to compare results from Full Genomes Corporation, FTDNA’s Big Y, and others who upload their raw data from NGS. There are presently 34 kits in the L21 Group, and 2 in the DF41 Group. (cross-posted).

Williamson
02-23-2014, 03:54 AM
I have uploaded my FGC results to YFull, and so far my experience has been a positive one. They downloaded my results a few days ago, and I received an email from them this morning with my password. After logging in I could view my SNPs, both public and private, as well as my STR results.

The STR results are nice. I have no idea what analysis is behind them, but I find them much more clear than the FGC analysis. The majority of STR counts are integral in YFull, while FGC reports decimal counts. I don't yet know if this is just a matter of a better definition for each STR, or if they are less precise and just drop the extra nucleotides. It's also really nice having a web interface. One can also list the STR results for all the men in a group, like the R-L21 group, and this displays all 481 STRs in a table similar to what we are used to seeing at FTDNA.

In terms of SNPs, YFull came up with 7 new private SNPs which I didn't have from FGC. There were all low quality SNPs (wouldn't pass FGC standards), and 4 of them had only a single read. I took at look at them myself and about 3 of them look to be possibilities which I'll likely send to YSEQ to double check. The other 4 don't look too promising, and generally involved misaligned reads.

One nice thing they did today was add some SNP names for some of my private SNPs. They were private only because they weren't already in their database from 1000 genomes or PGP. I had names for about a dozen of them from BISDNA, so I sent them the list and 10 minutes later it was done. I couldn't ask for more than that.

Although the webpages all look very good, they are very hard to navigate. There is a shocking lack of links between the webpages. I had to manually type addresses in the address bar to get around.

There is no link to e-mail YFull to ask questions. I hear they respond to their Facebook page, but I am one of the few people in North America without one.

You can export your SNP results. But, it would be great if there .csv files were comma separated, rather than semicolon separated. I know I'm getting a little picky now.

Overall I like the site, but the "Beta" in their title is there for a reason. I have no idea if they are going to start charging in the future or not, but right now it seems like a great place to organize our FGC or upcoming Big Y results. I would recommend those with FGC results to upload them, and join the appropriate groups.

Alex

Mikewww
02-26-2014, 01:45 AM
I noticed that the U106 guys send their Variant reports to one co-administrator who puts them in a giant spreadsheet. I'm not trying to detract from YFull. Its just that not everyone may submit to them if and when they start charging.

Is anyone interested in being the collector / central point for FGC reports for L21? Probably, someone is already doing it.

Williamson
02-26-2014, 03:02 AM
Hi Mike,

I have been doing just that for a while, although I obviously haven't been advertising as much as I should have been. I have been collecting the "variantCompare" files and loading them all into one big spreadsheet. So far I have 9 men in total.

http://www.littlescottishcluster.com/RL21/Files/SNPs.xlsx

There is also a link to this spreadsheet from

http://www.littlescottishcluster.com/othersites.html

The spreadsheet is nothing fancy, but does include the position of each SNP, it's names, the derived and ancestral states, as well as the confidence *s that FGC assigns to each SNP. I include all the mutations, both shared and private SNPs and INDELs. I also include information on which 1000 genomes samples also share the SNPs to allow for an easier identification of placement.

I encourage any L21 man who has tested at FGC to contribute their results. The more the merrier. If you wish to contribute your results, please e-mail them to me at scotsgenealogy@gmail.com.

I think Mark Jost and Robert Casey may be doing some analysis as well, but as far as I know, mine is the only big spreadsheet.

Alex

Muircheartaigh
02-26-2014, 01:56 PM
Hi Mike,

I have been doing just that for a while, although I obviously haven't been advertising as much as I should have been. I have been collecting the "variantCompare" files and loading them all into one big spreadsheet. So far I have 9 men in total.




I encourage any L21 man who has tested at FGC to contribute their results. The more the merrier. If you wish to contribute your results, please e-mail them to me at scotsgenealogy@gmail.com.

I think Mark Jost and Robert Casey may be doing some analysis as well, but as far as I know, mine is the only big spreadsheet.

Alex

Alex,

I'm in batch#5 of FGC and my results are due soon. When they arrive I'll make them available. My Big y results are scheduled for release in 2 days, as I ordered on the first morning they became available. Hopefully someone with the right skills can do a comparison of both sets of results. I expect there will be quite a number of common novel SNPs between the results, but with differing designations which will need to be cross referenced. It remains to be seen if FTDNA will be as comprehensive and transparent in their reporting as FGC have been in order to facilitate cross referencing.

ontheedge
02-26-2014, 08:35 PM
Hi Alex,
I am also in batch #5 and hopefully will have my results to pass onto you on 1st March???? My status bar is still stuck at around 50% so I’m not sure what that means. There has been no message from FG to keep me informed of progress. June last year, when I ordered this test, seems such a long time ago now! Btw is anyone else in batch 5 still on 50% or is it just me?
Eddy Edgecombe, DF13*

Celtarion
02-28-2014, 08:56 AM
Hi Alex,
I am also in batch #5 and hopefully will have my results to pass onto you on 1st March???? My status bar is still stuck at around 50% so I’m not sure what that means. There has been no message from FG to keep me informed of progress. June last year, when I ordered this test, seems such a long time ago now! Btw is anyone else in batch 5 still on 50% or is it just me?
Eddy Edgecombe, DF13*

Hi Eddy,

I'm in batch #5 as well, and the status bar hasn't changed, still at 50%. The only communication we had so far was through Facebook saying that the results were postponed till 1st of March...

Joss

Sealgair
02-28-2014, 08:59 PM
With raw data from BGI expected 01-March-2014. Hopefully we batch 5 people will start receiving the reports by the end of next week.

Rory Cain
02-28-2014, 10:33 PM
I have uploaded my FGC results to YFull
Alex

I tried to, but they keep asking for a link to my raw data. While I have a log-in to my kit number at FGC's website, this feature has never been functional.

Williamson
02-28-2014, 10:45 PM
I'm not sure what FGC has in mind for the future, but it is at least possible to ask them for your .bam file. I did that when I first got my results, and they provided me with a link from which I could download them. I don't know if they still offer that service, but you could try. Once you have your link, you could give it to YFull for them to download.

Rory Cain
03-02-2014, 07:02 AM
I'm not sure what FGC has in mind for the future, but it is at least possible to ask them for your .bam file. I did that when I first got my results, and they provided me with a link from which I could download them. I don't know if they still offer that service, but you could try. Once you have your link, you could give it to YFull for them to download.

Nice surprise. I discovered that FGC have in fact given members' pages some functionality & you can now view your report on-line. You just have to ask for it. I notice they activated yours too, Alex, although not that of our mutual friend David who has perhaps not asked for it. My haplogroupCompare spreadsheet has also been updated with one new SNP and one new InDel. As the SNP has three *** after it, I'm not convinced that it deserves a FGC number. My other private SNPs had nil or only one *. As Mark Jost pointed out, yseq can assess whether an iffy SNP is likely to be confirmed by Sanger sequencing.

I also discovered that once you give them approval to do so, the guys at full.com can contact FGC direct and upload your .bam file. That works for me, at least I hope it will.

Cofgene
03-02-2014, 12:25 PM
My haplogroupCompare spreadsheet has also been updated with one new SNP and one new InDel. As the SNP has three *** after it, I'm not convinced that it deserves a FGC number.

Maybe that FGC number comes from another sample?

Sealgair
03-02-2014, 03:57 PM
“Happy March 1st to everyone! Starting from this Monday the data will start to arrive to the FGC data analysis team and from there - after some time - to our customers. We are on schedule (+ two days).” Leon Kull on Full Genomes FB page

Rory Cain
03-04-2014, 04:05 AM
Maybe that FGC number comes from another sample?

If that were so, it would suggest that FGC erred in placing it amongst my private SNPs. However the possibility of human error should never be overlooked, sothanks for the reminder.

Cheers

Rory

Mag Uidhir 6
03-22-2014, 12:37 AM
Well, it's in finally!! kit no 226869 J. McGuire in L513-A-2-M (FGC id 6PN7S) I believe Mike has the data in his in box, but if not I have a separate copy that I can upload to the Yahoo group, if required.

I know the flood gates are truly opening for all of L21+ now ... finding the best comparative tool and methodology....whew. We shall see!!

Brad

ontheedge
03-29-2014, 11:29 AM
Does anyone know what the latest is on pending batch 5 FG results? The last I saw was that they were expected at the beginning of March. It seems that a few results have come through since but there must be many more still in the pipeline.

LarryWalker
04-01-2014, 07:47 PM
I've posted my "Variant Compare" spreadsheet online for the curious at http://rangebiome.org/FG-SNP1.xlsx , and forwarded the whole enchilada to Mark.:beerchug:
New location: https://fgc-production-results.s3.amazonaws.com/interpretation_results/29FKD.zip?Signature=pm0ESAdi4aS6rk8%2B2zv4YJWxJo8% 3D&Expires=1427917555&AWSAccessKeyId=AKIAJMZAJORUOB6GDCCA

LarryWalker
04-01-2014, 07:54 PM
Does anyone know what the latest is on pending batch 5 FG results? The last I saw was that they were expected at the beginning of March. It seems that a few results have come through since but there must be many more still in the pipeline.
http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=35575&viewfull=1#post35575

Kwheaton
04-12-2014, 09:47 PM
I have a Full Y U106 Z346 result I would like to share with the appropriate group Admin when it finishes posting. Please contact me. I have not kept up with the specifics of this group as much as U152 so I am looking to see would be closet to this particular branch and working on it directly with others.
Kelly

JamesKane
07-22-2014, 02:12 AM
I just noticed I never posted here when I ordered Full Y from FGC back in April. My sample sits in Batch #10 as of the last time the status was checked.

Mikewww
08-04-2014, 03:46 AM
Do you know who FGC ID # IFGWX is ? He would be a third L513 tester. I'm just trying to track down those results and compare them with the other FGC and Big Y guys in the "deeper dive" or "pass 2" analysis of NGS results.

Rory Cain
11-23-2014, 03:03 AM
What I can see so far is that I have 36 new SNPs numbered FGC5752 to FGC 5787, and eight new InDels numbered FGC5788 to FGC5795.

We now know that most of the above are common to the O'Cathain sept of East Galway. The most useful thus far is FGC5787 which splits L658. About 80% of L658 are also likely to be FGC5787+. It is old enough and has sufficient genetic diversity to meet ISOGG listing requirements, whenever ISOGG catch up on the backlog.

Mac von Frankfurt
09-04-2015, 09:32 PM
I don't know if this thread is still being actively used for its original purpose but I just dropped my sample in the mail to Virginia.

Rory Cain
09-10-2015, 08:51 PM
I don't know if this thread is still being actively used for its original purpose but I just dropped my sample in the mail to Virginia.

Mac, I don't know either but a Caine buddy returned his kit in July so we should both have some results to digest in about ...er, whatever it takes.

Mac von Frankfurt
09-14-2015, 12:14 AM
Mac, I don't know either but a Caine buddy returned his kit in July so we should both have some results to digest in about ...er, whatever it takes.

I just checked the FGC website and I have been assigned to Batch #9008 and my sample has been sent to the lab.

Rory Cain
09-14-2015, 03:44 AM
I just checked the FGC website and I have been assigned to Batch #9008 and my sample has been sent to the lab.

I received the following information from Fullgenomes re Y Elite 2.0, so I think the two kits I'm waiting on are in Batches 9004 & 9005:

"The read length is at least double Y Elite 1.0, ie > 200bp vs 100bp in Y Elite 1.0
Also, we are improving the technique in each run..."

"We're getting ready to incorporate some analyses we did of batch 9004 and should be returning results from Batch 9005 in about 35-45 days.

Mac von Frankfurt
09-14-2015, 04:11 AM
..."We're getting ready to incorporate some analyses we did of batch 9004 and should be returning results from Batch 9005 in about 35-45 days.

Thanks for the information. I like the implication they are making iterative improvements. Maybe I will see my results by year end.

Rory Cain
09-14-2015, 08:32 PM
Thanks for the information. I like the implication they are making iterative improvements. Maybe I will see my results by year end.
The kits I'm waiting on we're forwarded June & July, so it appears FGC have shortened the wait time from 6 months to 4 months.My own took 6 months in 2013.

I am wondering about the implications of FGC now getting twice the read length. My own kit gained 49 new SNPs and InDels. Then a close relation tested through Big Y, which only covered about 60%, which played havoc with comparison. Now it seems the new FGC tests may cover twice as much as my d Y Elite 1.0, which I'm not complaining about. But it may leave me comparing apples with oranges and lemons.

cairn
09-24-2015, 11:31 PM
Adding my kit to the tracking in this thread:
Sample arrived in Virginia on Sept 22, 2015
Current status is "working on sending it to the lab", Batch #9008.

I'm taking a guess that I'll get results in March 2016 - I'll be pleasantly surprised if I get them earlier than that.

Rory Cain
09-25-2015, 03:36 AM
Adding my kit to the tracking in this thread:
Sample arrived in Virginia on Sept 22, 2015
Current status is "working on sending it to the lab", Batch #9008.

I'm taking a guess that I'll get results in March 2016 - I'll be pleasantly surprised if I get them earlier than that.

Family Tree DNA, bigger a bigger organisation, send batches to their lab weekly. FGC being smaller and handling less volume appears to send batches about monthly. Therefore if you just miss the latest batch, you have to wait for the next one a month later, which adds about a month to the time elapsing between you returning your kit and when you receive your results.

From batching your kit, FTDNA can sometimes deliver results in about 30 days. But this appears to be very much a best case scenario. FGC's wait times used to be about six months when they used a Hong Kong lab but appear to be somewhat shorter now with their present lab. But allowing six months as you are would still be the wisest course.

Muircheartaigh
09-25-2015, 08:04 AM
I am wondering about the implications of FGC now getting twice the read length. My own kit gained 49 new SNPs and InDels. Then a close relation tested through Big Y, which only covered about 60%, which played havoc with comparison. Now it seems the new FGC tests may cover twice as much as my d Y Elite 1.0, which I'm not complaining about. But it may leave me comparing apples with oranges and lemons.

The main advantage of a longer read length is that it reduces the chance of ambiguous reports that are caused by misalignment of the reads against the reference I.e. placing reads in the wrong location on the Y. Results from the new tests may in fact help clear up some of your existing ambiguous results, which you no doubt have.

cairn
09-25-2015, 06:16 PM
FGC's wait times used to be about six months when they used a Hong Kong lab but appear to be somewhat shorter now with their present lab. But allowing six months as you are would still be the wisest course.

Thanks for the info about FGC's change of lab. I use sort of a reverse Scotty's Principle (http://www.urbandictionary.com/define.php?term=Scotty%20Principle) when setting my expectations to allow for lab delays, etc. A few recent tests I've done with FTDNA all took more than twice as long as expected despite (or, maybe, due to) being a larger company than FGC. I'll report back here when I get my results so others will know what to expect for future batches.

Mac von Frankfurt
09-25-2015, 07:47 PM
I am in batch #9008 as well. My status is "Your kit is currently being processed" with zero percent of the status bar colored. I am secretly hoping for results by Christmas but trying to keep my expectations at St. Patrick's Day.

Rory Cain
09-26-2015, 02:59 AM
The main advantage of a longer read length is that it reduces the chance of ambiguous reports that are caused by misalignment of the reads against the reference I.e. placing reads in the wrong location on the Y. Results from the new tests may in fact help clear up some of your existing ambiguous results, which you no doubt have.

Thanks for that explanation. Yes, I do have some ambiguous results and it gets expensive paying for Sanger confirmation. The guys who did Big Y as a cheaper alternative to Y Elite have even more ambiguous results and more no calls, so you get what you pay for.

Timeliness is not a FGC feature, but their greater coverage is. Y Elite is looking like the best test. After that it's worth paying Yfull $49 for their analysis so you get access to the best (IMHO) storage and retrieval database.

Rory Cain
10-11-2015, 06:51 AM
I am in batch #9008 as well. My status is "Your kit is currently being processed" with zero percent of the status bar colored. I am secretly hoping for results by Christmas but trying to keep my expectations at St. Patrick's Day.

I like the reliability of FGC results. The one thing they can't get right are estimates of time. Any estimate given must then be multiplied by a factor if your own choosing. So I am trying hard not to think of delivery dates at all, just the potential gains to be had from Batch 9005 results now pending.

cairn
10-20-2015, 03:55 PM
I just logged in to Full Genomes and found that my sample is now listed in batch #9007 (it was #9008). Maybe things are going more quickly now that they've got a second supplier (http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=114672&viewfull=1#post114672). The linked thread also mentions that batch #9005 data is being received this week.

Mac von Frankfurt, has your batch been changed as well?

Mac von Frankfurt
10-20-2015, 09:43 PM
Mac von Frankfurt, has your batch been changed as well?

Yes, I just checked and my batch number has been changed to #9007.

Rory Cain
10-27-2015, 12:32 AM
From another thread on Anthrogenica, FTDNA expected raw data back to them the week starting 20 Octover or the following week (ie this week), and that their analysis of the raw data would add one extra week. Further chat ges as follows:

Client: Good to hear, I am in Batch 9005.

Client: So a couple more weeks then?

FGC: November 7 would be a good estimate.

bfcockburn
11-05-2015, 09:14 PM
I have a kit in batch #9007 too. I figure that I'll be seeing results some time in the second half of November, given some of the times and batches mentioned in earlier postings.

cairn
11-06-2015, 12:02 AM
I have a kit in batch #9007 too. I figure that I'll be seeing results some time in the second half of November, given some of the times and batches mentioned in earlier postings.

Second half of November 2015 or 2016? ;)

I've been seeing results taking several months and batch 9005 is just coming in this week, so I think it'll be a few months yet before we see batch 9007 results. Not that I'd complain if results came in at the end of this month!

Rory Cain
11-14-2015, 08:53 PM
Second half of November 2015 or 2016? ;)

I've been seeing results taking several months and batch 9005 is just coming in this week, so I think it'll be a few months yet before we see batch 9007 results. Not that I'd complain if results came in at the end of this month!

Justin advised me that as the two sets of results in Batch 9007 that the O'Cathain group are awaiting were ordered in June, and as it still takes about 6 months, we might anticipate results about December.

Splitting the batch between two suppliers is an attempt to catch up a backlog. Catching up a backlog is a different thing to getting results quicker. So we won't get results any quicker, but hopefully not any later either.

Mac von Frankfurt
12-04-2015, 02:02 PM
I just checked my order history and I am still in Batch 9007. I read on another thread some samples had been moved to a different batch and are being sent to a new lab but it looks like I am still in Bath 9007 for now.

Mac von Frankfurt
02-13-2016, 06:30 PM
So maybe weeks instead of months now with a reported delivery date of 10 March for batch 9007.

Rory Cain
03-02-2016, 11:10 PM
In 2006 FTDNA released their Deep Clade product onto the market without the lab capacity to back it up. Customers were kept waiting all of that calendar year fir their results. I suggested that FTDBA take a less adversarial
approach to their competitors and start outsourcing so that at least their customers are kept satisfied.

While that didn't happen, they at least took the hunt about insufficient lab capacity to support their marketing, and purchased DNA Fingerprint from the Krahns and DNA Heritage from a small British outfit.

It is now déjà vu, 2006 all over again, with long lab delays. Every week the expected delivery date of tests gets pushed back by another fortnight. The "expected" delivery dates no longer have any credibility. FTDNA appears slow to recognise these choke-point crises and slow to react.

Despite the (valid) criticisms of long delays at FGC, I would suggest that those criticisms are somewhat negated by FTDNA's current inability to meet "expected" delivery dates. Right now you will wait as long at FTDNA as you would at FGC, and FGC delivers more SNPs in their Y Elite than does Big Y.

Mac von Frankfurt
03-29-2016, 02:22 AM
I shared my FGC Kit with the applicable L21 email and let Alex know.

FTDNA #B68484 I took a few STRs at FTDNA so I would show up on their charts.

I looked at the FGC files briefly but the only one I could make sense of started:


#Y-haplogroup match analysis based on FGC yKNOT utility
#uses ISOGG tree: http://www.isogg.org/tree/index.html

================================================== ==========

Match #1: R-CTS241

Williamson
03-29-2016, 04:24 AM
I shared my FGC Kit with the applicable L21 email and let Alex know.

You are R-L21>DF13>A4556/BY2868. You share about 10 SNPs with another fellow named James (kit 35874). I will hopefully have a chance to finish looking at your results this weekend.

Alex

Williamson
03-29-2016, 04:32 AM
Actually, I'm mistaken. You are now R-L21>DF13>Z39589>A4556/BY2868. Your test shows that the A4556 branch is positive for Z39589.

Alex