Low quality of Z49/Z68 SNPs?

[Petr]

Hello,

I'd like to ask what could be the reason of strange results of my L2 -> Z49/Z68 SNPs.

FTDNA BigY results:
L2: Genotype: ? Confidence: Unknown
Z49: Genotype: ? Confidence: Unknown
Z68: Genotype: ? Confidence: Unknown
pos. 2665967 Genotype: T Confidence: High

interpreted by FGC:
pos. 5755550 L2 • S139 (C->T): 37T 2C
pos. 28462237 Z49 unknown
pos. 21058323 Z68 unknown
pos. 2665967 S8183+ reliability warning level: **

interpreted by YFull:
pos. 5755550 L2 • S139 (C->T): 37T 2C
pos. 28462237 Z49 (G->T): no call position
pos. 21058323 Z68 • S485 (C->T): no call position
pos. 2665967 S8183 (G->T) 15T 1G

Geno 2.0 results:
L2,Y,T,T => positive
Z49,Y,T,G => ambiguous
Z68,Y,C,C => negative
S8183 not tested

23andMe
U152: rs1236440 Y 15333149 T
L2: rs2566671 Y 5755550 --
Z49, Z68 and S8183 not tested.

23andMe my father:
U152: rs1236440 Y 15333149 T
L2: rs2566671 Y 5755550 --
Z49, Z68 and S8183 not tested.

So:
L2 - sometimes (BigY FTDNA, 23andMe) no results
Z49 - BigY no call, Geno 2.0 ambiguous
Z68 - BigY no call, Geno 2.0 negative
S8183 - BigY only

So how it is with Z68? Ybrowse http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/?name=z68 shows:
count_derived: 0
count_tested: 0

YSEQ: does not offer Z68 SNP test.
FTDNA: does not offer Z68 SNP test.

Other samples analyzed by YFull, results for Z49 and Z68 from U152 group:
YF01527: ? ?
YF01555: ? ?
YF01461: - ?
YF01754: - ?
YF01926: ? ?
YF01489: ? ?
YF01733: + ?
YF01551: - ?
YF01647: - ?
YF02052: ? ?
It looks like NextGen tests analyzed by YFull often don't cover Z49 and no test cover Z68.

Just my observation, maybe with no importance. Now I'm waiting for BritainsDNA and FGS Elite test to see their results.

Petr

[haleaton]

I am L2+ but Z49-.
L2 was discovered in 23andMe though chip versions have changed. Still you can get No Call.
For some reason, the FTDNA BED file excludes L2 though other analysis shows that the data is there. Check VCF file which is text readable.
You can order any SNP from YSEQ and they will make it available.
Unfortunately, in making the Britains DNA chip the L2 "bead" ended up not working. In my case they did additional testing.
This may be same from Z49--I did a post months back about missing SNPs. Luck of the draw I guess.

My FGS Elite (BGI) had no problems with L2. My FGC BGI Bam data is YF01461 on your list. Some of the others are FTDNA Bams. My Big Y Bam is being analyzed by Yfull but has not been released yet pending evaluation of SNP that is positive in one test and negative in the otherr.

[Petr]

Britains DNA results:
L2: not tested
Z49: not tested
Z68 = S485: AG positive
S8183: AA positive

But what does mean "AG"? I have one Y chromosome, not two. And http://ybrowse.isogg.org/ shows C->T mutation and I have "AG"?

[Petr]

And YSEQ result:

Z68 ChrY 21058323 21058323 T+