Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > Z46512 > FGC78762 > ZZ19 > Z31644 > Z42772 > 8742535-G-GT > A431 > BY3288 > Y7365 > BY36464

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 STRBigY3
6136712-G-A 6268671-G-A A+
6210788-G-T 6342747-G-T IR3_Dst A*
6333948-A-C 6465907-A-C IR3_Dst A*
13687055-A-G 11531379-A-G A*
16150664-G-GA 14038784-G-GA P8_Dst 9×AA*
19934723-A-G 17822843-A-G P5_Prx A*
20731180-C-T 18569294-C-T P4_Prx A*
26060252-T-TGAA 23914105-T-TGAA P1_Y1 A*
26195062-G-A 24048915-G-A P1_Y1 A*
26426631-C-A 24280484-C-A P1_Y1 A*
21403584-G-C 19241698-G-C FT63483 YY+
21646081-C-T 19484195-C-T F24541 YY+
15485164-T-C 13373284-T-C Y93898 YY+
10767214-AT-A BY14605 +
3138966-A-G 3270925-A-G FT62380 +
3560221-G-C 3692180-G-C FT11634 +
4174022-T-A 4305981-T-A FT11826 +
4435934-T-G 4567893-T-G FT11892 +
5367166-CA-C 5499125-CA-C +
5820208-C-G 5952167-C-G FT62672 +
6030135-A-T 6162094-A-T FT12372 +
6401501-ATATCT-A 6533460-ATATCT-A +
6827530-T-C 6959489-T-C FT62737 Y+
7094190-T-C 7226149-T-C FT12535 YY+
7365700-T-C 7497659-T-C FT12580 YY+
8145706-A-T 8277665-A-T FT62854 YY+
8351496-G-T 8483455-G-T FT62865 YY+
8419138-G-C 8551097-G-C FT12715 YY+
8579286-G-T 8711245-G-T FT12741 YY+
9809107-G-A 9971498-G-A FT12841 YY+
9906470-C-T 10068861-C-T FT12854 Y+
13414504-G-A 11258828-G-A FT443544 +
11649010-G-A FT87681 +
14005325-A-C 11884619-A-C FT62990 YY+
14461606-A-G 12340879-A-G FT63035 YY+
14594457-C-G 12482657-C-G FT13058 YY+
14811473-C-T 12699544-C-T FT13091 YY+
15304154-C-T 13192253-C-T FT13156 YY+
15439526-T-C 13327646-T-C FT63098 YY+
15461292-C-T 13349412-C-T FT13179 YY+
15589671-T-C 13477791-T-C FT13197 YY+
15907106-C-G 13795226-C-G FT63139 YY+
17504994-G-T 15393114-G-T FT13458 Y+
17703115-C-T 15591235-C-T FT13487 YY+
18791876-C-G 16679996-C-G FT13622 Y+
19430281-A-C 17318401-A-C FT13719 YY+
22134267-A-T 19972381-A-T FT13960 YY+
22294349-T-G 20132463-T-G FT87682 DYZ19 +
22468678-G-T 20306792-G-T FT458906 DYZ19 +
22471700-A-G 20309814-A-G FT459296 DYZ19 +
22712326-A-T 20550440-A-T FT13997 YY+
23057899-G-C 20896013-G-C FT63598 YY+
23362732-C-T 21200846-C-T FT63618 Y+
23509701-G-A 21347815-G-A FT14112 YY+
28608268-T-C 26462121-T-C FT14233 +
28742555-T-C 26596408-T-C FT14271 +
28744239-A-T 26598092-A-T FT285153 +
22230117-G-A 20068231-G-A DYZ19 *
22302941-G-T 20141055-G-T FTB9148 DYZ19 *
27535811-G-T 25389664-G-T P1_Y2 *
25601455-A-AG 23455308-A-AG P1_gr1 **
13588207-C-T 11432531-C-T **
4200055-CAAAA-C 4332014-CAAAA-C 23×A**
3308771-TCTTTA-T 3440730-TCTTTA-T **
6482926-A-G 6614885-A-G **
10896436-T-G **
14763021-A-G 12651090-A-G **
16404914-GAATT-G 14293034-GAATT-G **
17110818-G-GA 14998938-G-GA **
17124590-A-G 15012710-A-G **
19609424-G-C 17497544-G-C P5_Prx **
19877707-A-G 17765827-A-G P5_Prx **
21861742-G-A 19699856-G-A **
22428938-A-T 20267052-A-T DYZ19 **
22437275-A-C 20275389-A-C FT456163 DYZ19 **
23520388-C-T 21358502-C-T **
23790541-G-A 21628655-G-A **
25894837-T-C 23748690-T-C P1_Y1 **
27474196-A-G 25328049-A-G P1_Y2 **
27699921-C-CAT 25553774-C-CAT P1_Y2 **
21142834-CAA-C,CAAA 18980948-CAA-C,CAAA 16×A***
6989125-A-C 7121084-A-C ***
28800099-ATG-A 26653952-ATG-A ***
2859982-T-C 2991941-T-C ***
2899928-G-A 3031887-G-A ***
3618436-AT-A 3750395-AT-A 9×T***
3873150-T-C 4005109-T-C ***
4196934-CA-C,CAA 4328893-CA-C,CAA 16×A***
4829411-C-A 4961370-C-A ***
6045251-T-C 6177210-T-C ***
6989124-A-C 7121083-A-C ***
7094839-C-T 7226798-C-T ***
13931739-CTTT-C,CTT 11811033-CTTT-C,CTT 22×T***
14123329-C-T 12002623-C-T ***
14123336-C-T 12002630-C-T ***
15762634-G-A 13650754-G-A ***
17403973-A-C 15292093-A-C ***
21405832-C-CA,CAA 19243946-C-CA,CAA 15×A***
21796008-C-A 19634122-C-A ***

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.