Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > L20/S144 > Exact position not yet finalized.

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
331038
56833784-T-A A*
26086775-T-C 23940628-T-C P1_Y1 A*
13687017-A-C 11531341-A-C A*
4370117-T-A 4502076-T-A FGC76633 A*
4417119-A-AT 4549078-A-AT A*
19730122-C-T 17618242-C-T P5_Prx A*
19606797-G-A 17494917-G-A P5_Prx YA*
25849594-C-G 23703447-C-G P1_Y1 A*
25849617-G-T 23703470-G-T P1_Y1 A*
18350433-T-G 16238553-T-G P6_Prx A*
26185388-C-A 24039241-C-A P1_Y1 A*
6251422-C-T 6383381-C-T IR3_Dst A*
26185436-G-A 24039289-G-A P1_Y1 A*
26095572-A-C 23949425-A-C P1_Y1 4×AAACA*
26408022-C-T 24261875-C-T P1_Y1 A*
56834130-T-C A*
21773731-A-G 19611845-A-G FT25640 YY+
13813109-A-G 11692403-A-G FT20620 +
9083605-C-T 9245996-C-T FT20307 Y+
21139515-A-G 18977629-A-G FT25130 YY+
8319474-A-G 8451433-A-G FT19788 YY+
19009933-G-C 16898053-G-C FT24602 YY+
10926056-C-T +
18709285-C-T 16597405-C-T FT24401 YY+
21186694-AAAGTAAATGTATC-A 19024808-AAAGTAAATGTATC-A +
17098815-T-C 14986935-T-C FT23213 YY+
14170024-A-G 12049318-A-G YY+
14243404-G-A 12122698-G-A YY+
14261813-G-A 12141107-G-A FT21194 YY+
7706539-C-T 7838498-C-T FT19380 YY+
17264234-C-T 15152354-C-T FT23340 YY+
17222324-G-A 15110444-G-A FT23308 Y+
15008254-TA-T 12896339-TA-T +
15044714-T-C 12932804-T-C FT21777 Y+
15055744-A-G 12943836-A-G FT21786 YY+
15058031-T-C 12946123-T-C FT21789 YY+
15776623-G-C 13664743-G-C FT22277 YY+
16061844-G-A 13949964-G-A YY+
16259470-C-T 14147590-C-T FT22564 YY+
16538259-G-A 14426379-G-A FT22793 YY+
17079102-A-T 14967222-A-T FT23193 YY+
8151937-C-A 8283896-C-A FT19674 YY+
5473348-T-C 5605307-T-C FT17611 +
7527993-G-A 7659952-G-A YY+
3401426-G-A 3533385-G-A FT15238 +
9022258-T-A 9184649-T-A A9224 Y+
15971217-A-G 13859337-A-G FT22396 YY+
16590638-C-T 14478758-C-T FT22840 YY+
16220933-G-A 14109053-G-A FT22526 YY+
23794465-T-C 21632579-T-C FT26833 Y+
3662969-G-A 3794928-G-A FT14379 +
23588272-G-T 21426386-G-T FT26735 YY+
23554436-A-T 21392550-A-T FT26707 YY+
10863157-G-A +
2840571-A-C 2972530-A-C FT14667 YY+
7326824-A-G 7458783-A-G FT19138 YY+
22208898-G-A 20047012-G-A FT25991 YY+
3483463-T-C 3615422-T-C FT15330 +
3765590-A-G 3897549-A-G FT15667 +
3961659-C-T 4093618-C-T FT15905 +
4064489-C-A 4196448-C-A FT16026 +
4207006-C-A 4338965-C-A FT16206 +
4463458-T-C 4595417-T-C FT16510 +
4487474-G-C 4619433-G-C FT16536 +
4815602-G-C 4947561-G-C FT16878 +
17189108-C-T 15077228-C-T FT23280 YY+
5790280-A-G 5922239-A-G FT18014 +
6063158-C-T 6195117-C-T FT18315 +
21854937-T-G 19693051-T-G FT25718 YY+
22231110-G-C 20069224-G-C DYZ19 *
22279576-G-A 20117690-G-A DYZ19 *
26079154-C-G 23933007-C-G P1_Y1 *
7508355-TTTCC-T 7640314-TTTCC-T L1403 13×TTCC*
10661754-C-T *
3662943-G-A 3794902-G-A FT44784 *
17654-T-C **
10065567-C-A 10227958-C-A **
22507655-A-T 20345769-A-T DYZ19 **
20040455-G-T 17928575-G-T P5_Prx **
24267153-G-T 22121006-G-T P3_b1 **
27883255-G-C 25737108-G-C P1_Y2 **
10065573-G-C 10227964-G-C **
2888739-C-T 3020698-C-T CTS311 **
10849819-TCATTCCATTC-T **
13611328-C-A 11455652-C-A **
11665038-C-T **
18017150-T-C 15905270-T-C BY31594 ***
23455053-AT-A,ATT 21293167-AT-A,ATT 14×T***
8389569-CTTT-C,CTT 8521528-CTTT-C,CTT 25×T***
28522751-CTTT-C 26376604-CTTT-C 17×T***
16842867-ATGTGTG-A 14730987-ATGTGTG-A 22×TG***
14836360-CA-C 12724427-CA-C ***
10756852-T-C ***
22981819-TAA-T,TA 20819933-TAA-T,TA 15×A***
14319467-A-G 12198761-A-G ***
22485404-A-T 20323518-A-T DYZ19 ***
4393077-C-T 4525036-C-T ***
2928723-G-GTTTTTTTT 3060682-G-GTTTTTTTT ***
3253843-AAAAAT-A,AAAAAA 3385802-AAAAAT-A,AAAAAA ***
7203659-A-G 7335618-A-G ***
10041550-C-A 10203941-C-A ***
10625249-T-A ***
22485405-A-T 20323519-A-T DYZ19 ***

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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 3310381517560295117518373763
Used in age calculations1517560295117518373763
Counts of SNPs34
Variant counts last updated 2019-10-20 02:34:00.



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