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Petr
03-01-2017, 10:08 PM
Hello,

does anybody know what does mean rs200511657?

I see it in the U152 FTDNA project:

U152> L2> Z41150> Z49,Z68> rs200511657> S8183,BY3626> Y4356>

If I check the position of rs200511657:
http://ybrowse.org/gb2/gbrowse/chrY/?name=rs200511657
https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=200511657
I see that it is 10,023,952.

But according to U152 project ALL U152 samples have "G" (REF) at position 10023952 and none "C" (ALT).

I don't understand.

Maybe it should mean indel 10023952-GTCTC-G as it is described here: http://www.ytree.net/DisplayTree.php?blockID=1770&star=false ?

Is it correct to use rs200511657 rsid for this indel?

Petr

MitchellSince1893
03-03-2017, 12:43 AM
Hello,

does anybody know what does mean rs200511657?

I see it in the U152 FTDNA project:

U152> L2> Z41150> Z49,Z68> rs200511657> S8183,BY3626> Y4356>

If I check the position of rs200511657:
http://ybrowse.org/gb2/gbrowse/chrY/?name=rs200511657
https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=200511657
I see that it is 10,023,952.

But according to U152 project ALL U152 samples have "G" (REF) at position 10023952 and none "C" (ALT).

I don't understand.

Maybe it should mean indel 10023952-GTCTC-G as it is described here: http://www.ytree.net/DisplayTree.php?blockID=1770&star=false ?

Is it correct to use rs200511657 rsid for this indel?

Petr

Standby, ironically this very issue is currently being discussed between FTDNA and U152 admin. We should have an answer soon.

Petr
03-03-2017, 07:58 AM
It is interesting that my WGS 15x result does not show this indel, this is from YFull U152 project:

14342

YF01551 = my FTDNA BigY
YF02970 = my FGC Elite
YF04805 = my FGC WGS 15x



And it is interesting that the same indel:
14343
has two different definitions and two different names.

At first FGC defined it as FGC20812:
http://ybrowse.org/gb2/gbrowse/chrY/?name=FGC20812
Position: ChrY:6762873..6762876 (+ strand)
mutation: AATA to del

Later FTDNA defined it as BY3626
http://ybrowse.org/gb2/gbrowse/chrY/?name=BY3626
Position: ChrY:6762871..6762875 (+ strand)
mutation: CAAAT to C

It looks like YFull defines no indels.

MitchellSince1893
03-10-2017, 02:57 AM
The position is 10023952 10023952 GTCTC-G

http://ytree.net/DisplayTree.p hp?blockID=1770&star=false

http://ybrowse.org/gb2/gbrowse _details/chrY?ref=ChrY;start= 10023952;end=10023952;name= rs200511657;class=Sequence; feature_id=483751;db_id=chrY% 3Adatabase

rs200511657 is a marker that Alex Williamson will call but FTDNA will not.

According to FTDNA the data associated with this marker is rather "junky" and is one that will not be called in BigY results, thus FTDNA prefers to not include it on their haplotree at this time. Alex has different rules for inclusion on his Bigtree.

The U152 project admin have decided to include it as well.

Petr
11-25-2017, 06:40 PM
I have noticed that in the new hg38 VCF files is this indel shifted 6 bp to the right and it look like this:

10186352 TCTCT to T

And probably due to aggressive filtering,
8TCTCT 5T changed to 3T (kit 195364)
9TCTCT 19T changed to 19T (kit 348782)

If I understand correctly, indels are not displayed correctly at FTDNA website at present.