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View Full Version : Geno2+ raw data sometimes uses other strand?



lgmayka
03-21-2016, 03:17 PM
I am trying to decipher someone's Geno2+ raw data (downloaded from FTDNA). It seems that many of the alleles are recorded on the "wrong" strand. For example:
S17076 is A>C, but he has GG
FGC12085 is G>A, but he has TT
S15817 is A>C, but he has GG
S12235 is T>C, but he has GG
S19015 is C>T, but he has AA

Are other people seeing the same thing?

Petr
03-21-2016, 04:04 PM
IIRC it was the same with the original Geno 2.0 with both Y and mt markers.

ArmandoR1b
03-21-2016, 04:26 PM
Nevermind: I misread your post

wombatofthenorth
04-12-2016, 12:27 AM
IIRC it was the same with the original Geno 2.0 with both Y and mt markers.

Does anyone know if BY2171 is one of the ones that needs to be read backwards?
FTDNA shows it as untested (negative?) but value is AA and ISOGG SNP Lookup says A is derived.

ArmandoR1b
04-12-2016, 02:14 AM
Does anyone know if BY2171 is one of the ones that needs to be read backwards?
FTDNA shows it as untested (negative?) but value is AA and ISOGG SNP Lookup says A is derived.
BY2171 is 23615856 T to A (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=23615856;end=23615856;name=BY2 171;class=Sequence;feature_id=97733;db_id=chrY%3Ad atabase). So that should show as positive.

What lgmayka is describing and what you are describing are two different things. He is saying that the SNPs that he listed don't have either of the alleles they are supposed. Your file has the allele listed twice because "While the Y chromosome is a single copy piece of DNA, the Illumina software used to call alleles is designed for autosomal markers which come in two copies. Hence when AA or GG are given, it means A or G, respectively." The quoted information is from a Chromo2 spreadsheet.

wombatofthenorth
04-12-2016, 02:51 AM
BY2171 is 23615856 T to A (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=23615856;end=23615856;name=BY2 171;class=Sequence;feature_id=97733;db_id=chrY%3Ad atabase). So that should show as positive.

What lgmayka is describing and what you are describing are two different things. He is saying that the SNPs that he listed don't have either of the alleles they are supposed. Your file has the allele listed twice because "While the Y chromosome is a single copy piece of DNA, the Illumina software used to call alleles is designed for autosomal markers which come in two copies. Hence when AA or GG are given, it means A or G, respectively." The quoted information is from a Chromo2 spreadsheet.

What I meant if if they read it from the opposite strand doesn't A become T so in that case TT would be the positive instead of AA.
That would explain why FTDNA seems to have treated it as a negative (by pretending it wasn't tested).
Otherwise I don't know why they failed to mark it as positive. The only other reason is if they found out it's not reliable.

wombatofthenorth
06-10-2016, 11:37 PM
What I meant if if they read it from the opposite strand doesn't A become T so in that case TT would be the positive instead of AA.
That would explain why FTDNA seems to have treated it as a negative (by pretending it wasn't tested).
Otherwise I don't know why they failed to mark it as positive. The only other reason is if they found out it's not reliable.

FTDNA finally got back to me and they and Geno 2.0 NG results were correct in not listing my dad as R-BY2171 since he is negative for it. It turns out that that spot needs to be read opposite strand so his AA is really TT and ancestral using the traditional strand. FTDNA says they will eventually get around to swapping the strands for such SNPs in the RAW download data but it may take a while to get all of them switched. So the RAW data can sometimes have opposite strand results listed although the tree and results given use code that knows what is what and work fine, especially on the Geno 2.0 NG site. But you have to use care at times trying to interpret some of the Y and mtDNA RAW data yourself (they also pointed out one reversed mtDNA spot too).