Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > ZZ10 > Z253 > Z2534 > ZZ5 > Z2185 > BY44331 > A287

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
2654262-G-A 2786221-G-A BY2898 Y+
6859429-T-C 6991388-T-C BY4294 YY+
7245482-C-G 7377441-C-G BY12565 YY+
7402565-T-G 7534524-T-G BY17940 YY+
7521474-G-A 7653433-G-A BY12566 YY+
7950574-T-C 8082533-T-C BY12567 YY+
8185673-G-T 8317632-G-T BY12568 YY+
8433911-G-C 8565870-G-C BY12569 YY+
8466194-A-AAAATAAAT 8598153-A-AAAATAAAT 11×AAAT+
8618063-G-C 8750022-G-C BY12570 YY+
8701010-G-A 8832969-G-A BY12571 YY+
8837956-A-G 8969915-A-G BY12572 YY+
9091938-A-T 9254329-A-T BY12573 Y+
9648424-A-C 9810815-A-C BY4295 IR3_Prx +
13658388-A-G 11502712-A-G BY12574 +
13691096-T-G 11535420-T-G BY12575 +
13843048-GTGGAA-G 11722342-GTGGAA-G +
14168347-G-A 12047641-G-A BY12576 YY+
15359395-T-C 13247515-T-C BY12577 YY+
15518754-A-G 13406874-A-G BY12578 YY+
15754692-C-T 13642812-C-T Y94686 YY+
15970968-G-T 13859088-G-T BY12579 YY+
16650674-G-A 14538794-G-A BY12580 YY+
16820679-C-G 14708799-C-G BY12581 YY+
17263638-G-C 15151758-G-C BY12582 YY+
18083707-T-C 15971827-T-C BY12583 YY+
18774040-A-G 16662160-A-G BY12584 YY+
19466851-G-A 17354971-G-A BY12585 YY+
21902711-C-T 19740825-C-T PR6936 YY+
22004215-T-A 19842329-T-A BY12586 YY+
22186305-G-C 20024419-G-C BY12587 YY+
22263230-C-G 20101344-C-G BY12588 DYZ19 +
23063244-C-T 20901358-C-T BY12590 YY+
23523159-T-G 21361273-T-G BY12591 YY+
23839176-T-A 21677290-T-A BY12592 Y+
23058442-G-T 20896556-G-T CTS11291 PF4615 YY*
13801029-G-A 11680323-G-A **
13801036-A-G 11680330-A-G **
14104315-A-G 11983609-A-G CTS1870 M3916 Z1741 **
16583227-C-T 14471347-C-T PR5867 FGC21951 **
6018602-G-T 6150561-G-T K89 **
6708988-A-ATTGC 6840947-A-ATTGC **
23115951-C-G 20954065-C-G **
23199656-C-T 21037770-C-T CTS11634 **
28091393-GAGAT-G 25945246-GAGAT-G P1_Y2 5×AGAT**
28597053-G-A 26450906-G-A BY44276 **
7269601-C-T 7401560-C-T ***
13668024-T-A 11512348-T-A ***
13847199-GAATGGACTCA-G 11726493-GAATGGACTCA-G ***
9307400-G-C 9469791-G-C ***
15592550-C-A 13480670-C-A 22×A***
16107473-C-T 13995593-C-T P8_Prx ***
18378987-TGC-T 16267107-TGC-T P6_Prx ***
13452389-T-C 11296713-T-C ***
22305502-G-T 20143616-G-T DYZ19 ***
22360716-A-C 20198830-A-C DYZ19 ***
28800289-G-A 26654142-G-A ***
58908929-C-T 56681942-G-A ***
13839630-G-T 11718924-G-T ***
58821963-C-A 56768908-G-T ***
7651836-A-G 7783795-A-G M4998 ***
22454945-A-C 20293059-A-C DYZ19 ***
25524693-C-T 23378546-C-T A10478 P1_gr1 33×T***
16757043-A-ATTT 14645163-A-ATTT 27×T***
58865975-G-T 56724896-C-A ***
58912863-G-C 56678008-C-G ***
26834853-AAAGG-A 24688706-AAAGG-A P1_g2 11×AAGG***
13703625-C-T 11547949-C-T ***
13866449-C-G 11745743-C-G ***
13458593-T-C 11302917-T-C ***
15815336-C-CA 13703456-C-CA 57×A***
13825038-C-G 11704332-C-G ***
24300813-CT-C 22154666-CT-C P3_t1 25×T***
10020624-C-T 10183015-C-T ***
13801020-A-T 11680314-A-T ***
13866442-T-TCAGAATCAAA 11745736-T-TCAGAATCAAA ***
24905127-AAT-A 22758980-AAT-A g1 9×AT***
13662007-G-A 11506331-G-A BY192390 ***
13141190-TTCCATTCCAC-T 10630676-TTCCATTCCAC-T ***
13141209-A-T 10630695-A-T ***
14612238-G-T 12500444-G-T ***
13668022-T-A 11512346-T-A ***
58866107-G-C 56724764-C-G ***
22449257-C-G 20287371-C-G DYZ19 ***
13452845-C-CCA,G 11297169-C-CCA,G ***
14612234-G-T 12500440-G-T ***
13139527-T-A 10629013-T-A ***
58821938-G-A 56768933-C-T ***
58821953-G-A 56768918-C-T ***
58821957-G-C 56768914-C-G ***
25870956-CATCT-C 23724809-CATCT-C P1_Y1 5×ATCT***
14612173-A-G 12500379-A-G CTS2998 ***
7651728-T-C 7783687-T-C ***
7651734-T-G 7783693-T-G ***
7651738-C-G 7783697-C-G ***
13669794-C-T 11514118-C-T FT447790 ***
13669797-C-A 11514121-C-A BY210806 ***
58856027-A-C 56734844-T-G ***
28785755-TGGAAC-T 26639608-TGGAAC-T ***
13865775-G-C 11745069-G-C ***
13800994-G-A 11680288-G-A ***
13801013-G-A 11680307-G-A ***
13801170-A-T 11680464-A-T ***
13447080-A-G 11291404-A-G ***
13805993-G-T 11685287-G-T ***
13464633-G-A 11308957-G-A ***
22305512-A-T 20143626-A-T DYZ19 ***
20332111-C-CAA 18170225-C-CAA P5_Dst 30×A***
24192237-CA-C 22046090-CA-C P3_b1 22×A***
7474294-T-C 7606253-T-C ZS3822ZS3822 IR1_L ***
9351191-T-TAC 9513582-T-TAC ***
13450900-T-C 11295224-T-C ***
13649013-A-C 11493337-A-C ***
13688651-C-G 11532975-C-G ***
13696373-T-G 11540697-T-G ***
13706897-T-G 11551221-T-G ***
13714245-G-C 11558569-G-C ***
13716711-G-GGATTC 11561035-G-GGATTC ***
13717322-A-C 11561646-A-C ***
13722184-G-A 11566508-G-A ***
13839649-TCGACG-T 11718943-TCGACG-T ***
13865776-A-T 11745070-A-T ***
13869510-GA-G 11748804-GA-G ***
13869513-T-A 11748807-T-A ***
18306144-C-T 16194264-C-T P6_Prx ***
19669229-C-CA 17557349-C-CA P5_Prx 8×A***
19866971-CAA-C 17755091-CAA-C P5_Prx 16×A***
19995323-T-A 17883443-T-A P5_Prx ***
22223591-A-T 20061705-A-T DYZ19 ***
22224827-G-A 20062941-G-A BY34425 DYZ19 ***
22232040-C-G 20070154-C-G DYZ19 ***
22245778-G-A 20083892-G-A DYZ19 ***
22245794-A-G 20083908-A-G DYZ19 ***
22256756-G-C 20094870-G-C DYZ19 ***
22265312-G-T 20103426-G-T DYZ19 ***
22265957-T-A 20104071-T-A DYZ19 ***
22277772-T-C 20115886-T-C ZS4707 DYZ19 ***
22307866-G-T 20145980-G-T DYZ19 ***
22312913-C-A 20151027-C-A BY25064 DYZ19 ***
22422897-G-C 20261011-G-C DYZ19 ***
22447879-A-C 20285993-A-C BY219925 DYZ19 ***
22453758-C-A 20291872-C-A DYZ19 ***
22454959-C-T 20293073-C-T DYZ19 ***
24167652-C-T 22021505-C-T P3_b1 ***
24348786-T-C 22202639-T-C P3_t1 ***
25176880-TG-T 23030733-TG-T g1 ***
25176882-A-T 23030735-A-T g1 ***
25176883-G-T 23030736-G-T g1 ***
25257141-C-T 23110994-C-T P2_r1 ***
25266999-GAA-G 23120852-GAA-G P2_r1 17×A***
26122000-ATT-A 23975853-ATT-A P1_Y1 18×T***
26143072-C-A 23996925-C-A P1_Y1 ***
58820565-A-C 56770306-T-G ***
13648959-TAAAGG-T 11493283-TAAAGG-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.