Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z16500 > A9029

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STRFTDNA
2892461-T-C 3024420-T-C B363 YY+
7147219-G-A 7279178-G-A Y45694 YY+
7522547-G-A 7654506-G-A Y46062 YY+
7626386-C-T 7758345-C-T Y46190 YY+
7855725-A-C 7987684-A-C Y46522 YY+
8156960-C-T 8288919-C-T BY42749 YY+
13854112-G-A 11733406-G-A Y48763 +
14184752-C-A 12064046-C-A Y49102 YY+
14842176-GGT-G 12730243-GGT-G +
15510918-C-T 13399038-C-T Y50768 YY+
16337650-A-G 14225770-A-G Y51717 YY+
16697623-T-C 14585743-T-C Y52217 YY+
16771206-T-C 14659326-T-C Y52302 YY+
16813750-G-A 14701870-G-A Y52370 YY+
17281266-CTGTT-C 15169386-CTGTT-C FGC20749 5×TGTT+
17310568-G-A 15198688-G-A Y53061 YY+
17328821-G-A 15216941-G-A Y53084 YY+
17466284-G-A 15354404-G-A Y53303 YY+
17705286-A-G 15593406-A-G Y53604 YY+
17712363-A-G 15600483-A-G BY116862 YY+
18253104-C-T 16141224-C-T BY121214 Y+
18614044-A-G 16502164-A-G Y54674 YY+
19234632-TA-T 17122752-TA-T +
21636045-T-C 19474159-T-C Y56986 YY+
21757569-A-G 19595683-A-G Y57160 YY+
21936864-T-A 19774978-T-A Y57412 YY+
22461684-A-T 20299798-A-T BY220725 DYZ19 +
22487253-G-C 20325367-G-C BY48305 DYZ19 +
22487254-G-T 20325368-G-T BY24651 DYZ19 +
22651840-T-C 20489954-T-C Y58093 YY+
23300302-T-G 21138416-T-G Y59006 YY+
23401772-C-T 21239886-C-T Y59124 YY+
23746528-C-T 21584642-C-T Y+
23968194-C-T 21822047-C-T ZS9769 Y+
23980764-G-A 21834617-G-A Y59655 Y+
23984968-G-A 21838821-G-A Y59663 Y+
24280690-T-G 22134543-T-G BY226033 P3_t1 +
27894290-A-G 25748143-A-G ZS4479 P1_Y2 +
5905010-A-C 6036969-A-C BY58936 **
9486071-C-A 9648462-C-A BY79825 **
14611844-G-A 12500050-G-A CTS2994 **
22362931-T-C 20201045-T-C DYZ19 **
28809430-TGGAATGTAAG-T 26663283-TGGAATGTAAG-T ***
58819367-C-A 56771504-G-T ***
13860204-T-C 11739498-T-C BY49167 ***
28784403-ATGTAG-A,ATGGAG 26638256-ATGTAG-A,ATGGAG ***
13843993-T-TCAACC 11723287-T-TCAACC ***
13680799-C-A 11525123-C-A ***
13689500-T-G 11533824-T-G ***
13664681-T-A,G 11509005-T-A,G ***
6233487-G-A 6365446-G-A IR3_Dst ***
6381642-G-T 6513601-G-T ***
9318131-C-T 9480522-C-T ***
9519818-T-TTC 9682209-T-TTC ***
9978045-TAA-T 10140436-TAA-T ***
13322034-T-C 11166358-T-C ***
13457773-TTCCACTCGGA-T 11302097-TTCCACTCGGA-T ***
13652203-A-C 11496527-A-C ***
13676718-T-G 11521042-T-G ***
13743933-G-A 11588257-G-A ***
13801201-A-G 11680495-A-G ***
13808674-G-A 11687968-G-A ***
13847227-T-A 11726521-T-A ***
13852011-C-CGATTG 11731305-C-CGATTG 11×GAATG***
13857520-A-G 11736814-A-G ***
13857941-G-GAATGC 11737235-G-GAATGC ***
13858315-G-GAATGC 11737609-G-GAATGC ***
13866709-GGAAAC-G 11746003-GGAAAC-G ***
14172725-G-T 12052019-G-T ***
14172726-A-C 12052020-A-C ***
14172729-TTTTAC-T 12052023-TTTTAC-T ***
14937821-A-T 12825886-A-T ***
19577001-T-C 17465121-T-C P5_Prx ***
19779665-CT-C 17667785-CT-C P5_Prx ***
19892867-TG-T 17780987-TG-T P5_Prx ***
20326005-GAC-T 18164119-GAC-T P5_Dst ***
20663687-T-C 18501801-T-C P4_Prx ***
20679953-T-C 18518067-T-C P4_Prx ***
21148632-G-A 18986746-G-A ***
22242420-G-T 20080534-G-T DYZ19 ***
22280332-C-A 20118446-C-A DYZ19 ***
22316021-G-A 20154135-G-A DYZ19 ***
22345277-G-A 20183391-G-A DYZ19 ***
22427348-G-C 20265462-G-C DYZ19 ***
22437630-G-T 20275744-G-T BY43806 DYZ19 ***
22452845-G-C 20290959-G-C DYZ19 ***
22459196-C-G 20297310-C-G DYZ19 ***
24230559-A-G 22084412-A-G P3_b1 ***
25196438-T-C 23050291-T-C g1 ***
25207883-G-A 23061736-G-A P2_r1 ***
25946015-C-A 23799868-C-A P1_Y1 ***
26053424-A-T 23907277-A-T P1_Y1 ***
26068243-C-T 23922096-C-T ZS2303 P1_Y1 ***
26139717-A-C 23993570-A-C P1_Y1 ***
26155127-G-T 24008980-G-T P1_Y1 ***
26228684-TC-T 24082537-TC-T P1_Y1 ***
58830453-GCATTC-G 56760393-CAATGG-C 4×CATTC***
58973998-T-G 56827851-T-G ***
13450318-T-C,G 11294642-T-C,G ***
13664688-C-A,G 11509012-C-A,G ***
14937823-A-ATTTTCTTTTC,C 12825888-A-C 10×TTTTC***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

Mutation Notes:

Manual18286151-G-A16174271-G-A20 unambiguously positioned reads and all show A. The other couple dozen reads are split G and A.