Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > Z193 > Z40483 > BY3654 > BY3627

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
2668687-G-A 2800646-G-A Y81178 YY+
2731342-G-A 2863301-G-A Y81313 YY+
6859491-C-T 6991450-C-T Y82718 YY+
7074769-T-C 7206728-T-C Y83307 YY+
7585144-T-C 7717103-T-C Y84376 YY+
7614831-T-C 7746790-T-C Y84447 YY+
8486570-G-A 8618529-G-A ZS11566 YY+
8700576-G-C 8832535-G-C Y87766 YY+
14288333-A-T 12167627-A-T BY38865 YY+
15163229-G-A 13051315-G-A Y93174 YY+
15711599-T-G 13599719-T-G Y94522 YY+
15988842-G-T 13876962-G-T BY105337 YY+
16391476-A-G 14279596-A-G BY107456 YY+
16483145-G-C 14371265-G-C Y96477 YY+
17649121-G-T 15537241-G-T Y99814 YY+
18197460-A-G 16085580-A-G BY120763 YY+
18576027-A-G 16464147-A-G Y102141 YY+
18649210-T-C 16537330-T-C Y102317 YY+
19233430-G-T 17121550-G-T Y104111 YY+
21309217-GGAGTC-G 19147331-GGAGTC-G +
21930211-G-T 19768325-G-T Y107925 YY+
22120717-C-T 19958831-C-T Y108444 YY+
22235896-G-A 20074010-G-A BY38866 DYZ19 +
22362132-A-G 20200246-A-G BY217679 DYZ19 +
22537479-A-G 20375593-A-G Y+
23273890-T-A 21112004-T-A Y111155 YY+
23592878-G-C 21430992-G-C Y111986 YY+
23869966-G-A 21708080-G-A BY148620 Y+
27369543-T-A 25223396-T-A PR4033 P1_g3 **
28578357-T-A 26432210-T-A CTS12330 PF1317 **
7113693-G-A 7245652-G-A PR870 **
23007120-G-T 20845234-G-T **
24888857-C-T 22742710-C-T BY38869 g1 **
13140112-A-T 10629598-A-T ***
13450765-A-C 11295089-A-C ***
13839858-A-T 11719152-A-T BY91101 ***
13801177-T-A 11680471-T-A ***
13649030-G-A 11493354-G-A ***
26089061-C-A 23942914-C-A P1_Y1 20×A***
13838239-GTGGGA-A,G 11717533-GTGGGA-A,G ***
26089060-T-A 23942913-T-A P1_Y1 ***
13677893-T-G 11522217-T-G ***
13694236-T-C 11538560-T-C ***
13694270-A-T 11538594-A-T ***
13456370-C-A 11300694-C-A ***
13868276-A-G 11747570-A-G ***
13858600-T-G 11737894-T-G ***
19868145-CTTT-C 17756265-CTTT-C P5_Prx 31×T***
10037237-T-TG 10199628-T-TG ***
27810250-A-AAG 25664103-A-AAG P1_Y2 ***
22254417-A-G 20092531-A-G FGC78609 DYZ19 ***
13677829-GA-G 11522153-GA-G ***
13677839-G-T 11522163-G-T ***
22438508-T-G 20276622-T-G DYZ19 ***
13869618-T-A 11748912-T-A ***
26152185-T-TTC 24006038-T-TTC P1_Y1 ***
6001170-G-C 6133129-G-C ***
6001182-C-T 6133141-C-T ***
22438406-G-A 20276520-G-A DYZ19 ***
22284038-G-T 20122152-G-T DYZ19 ***
28103949-C-T 25957802-C-T P1_Y2 22×T***
10020493-G-T 10182884-G-T ***
13143783-TGCACTGCACA-C,T 10633269-TGCACTGCACA-C,T ***
20211758-AT-A,ATT 18049872-AT-A,ATT P5_Dst 14×T***
5471894-GAAAAAGAA-G 5603853-GAAAAAGAA-G ***
6309478-G-A 6441437-G-A IR3_Dst ***
7458107-G-A 7590066-G-A FT374560 IR1_L ***
9227849-G-A 9390240-G-A ***
13457413-ATTCCT-A 11301737-ATTCCT-A ***
13676723-A-C 11521047-A-C ***
13694230-T-TGGAAA 11538554-T-TGGAAA ***
13851694-C-A 11730988-C-A FT233030 ***
16104033-C-A 13992153-C-A P8_Prx ***
17994873-AC-A,AA 15882993-AC-A,AA P7_Prx ***
18313374-C-T 16201494-C-T P6_Prx ***
19744991-ATTTT-A 17633111-ATTTT-A P5_Prx 23×T***
19931529-G-A 17819649-G-A P5_Prx ***
22260339-C-T 20098453-C-T DYZ19 ***
22284620-T-A 20122734-T-A DYZ19 ***
22285474-AG-A 20123588-AG-A DYZ19 ***
22307767-G-C 20145881-G-C DYZ19 ***
22422694-G-T 20260808-G-T DYZ19 ***
22436410-G-T 20274524-G-T DYZ19 ***
22449327-C-T 20287441-C-T DYZ19 ***
22464078-C-T 20302192-C-T BY38868 DYZ19 ***
24259569-G-A 22113422-G-A P3_b1 ***
24831126-T-A 22684979-T-A P3_b2 ***
25865546-A-G 23719399-A-G P1_Y1 ***
25872134-G-A 23725987-G-A P1_Y1 ***
26013149-C-T 23867002-C-T P1_Y1 ***
26066685-G-A 23920538-G-A P1_Y1 ***
26914080-C-CTTT 24767933-C-CTTT P1_r3 37×T***

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.