Tree Position

R-P312/S116 > DF19/S232 > DF88 > FGC11833 > Z17110 > S4268

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
16252782-T-C 14140902-T-C Y13844 Z21737 YY+
21973658-G-A 19811772-G-A Y13848 Z21749 YY+
7555859-C-T 7687818-C-T Y13215 Z21729 YY+
8032787-C-T 8164746-C-T Y13216 Z21730 YY+
8142418-A-T 8274377-A-T Y13217 Z21731 YY+
21422605-C-A 19260719-C-A Y56663 YY+
8480188-C-T 8612147-C-T Y13836 Z21733 YY+
8674341-G-A 8806300-G-A Y13219 Z21734 YY+
9737441-C-T 9899832-C-T Y13837 Z21735 IR3_Prx +
15307522-T-TCTCCC 13195624-T-TCTCCC 5×CTCCC+
15670386-T-C 13558506-T-C Y13220 Z21736 Y+
16252786-TC-T 14140906-TC-T +
6872457-C-T 7004416-C-T Y45398 YY+
16360920-A-G 14249040-A-G S8139 YY+
16544788-G-T 14432908-G-T Y13222 Z21739 YY+
16719314-T-G 14607434-T-G Y13223 Z21740 YY+
16897014-A-G 14785134-A-G Y13224 Z21741 YY+
17573541-A-G 15461661-A-G Y13225 Z21742 YY+
17869267-C-A 15757387-C-A Y13841 Z21743 YY+
19120044-A-T 17008164-A-T Y13846 Z21744 YY+
19243075-AG-A 17131195-AG-A +
19360564-C-A 17248684-C-A Y13847 Z21746 YY+
19397208-TTCTA-T 17285328-TTCTA-T +
21687582-A-T 19525696-A-T Y57072 YY+
6995607-T-G 7127566-T-G Y13843 Z21728 YY+
8231493-G-A 8363452-G-A Y13218 Z21732 YY+
3545293-G-T 3677252-G-T Y13835 Z21727 +
22487356-G-A 20325470-G-A DYZ19 +
24422366-G-A 22276219-G-A Y13838 Z21753 Y+
23799902-A-T 21638016-A-T Y13849 Z21752 Y+
23297025-C-A 21135139-C-A S8137 YY+
21560112-GT-G 19398226-GT-G +
22459548-C-T 20297662-C-T Z21750 DYZ19 +
22478818-A-T 20316932-A-T Z21751 DYZ19 +
22537242-T-A 20375356-T-A PF2193 **
22424387-G-C 20262501-G-C DYZ19 **
13196297-T-C 11040621-T-C PF465 **
13454779-A-T 11299103-A-T **
14506747-C-A 12394952-C-A **
22236337-T-TCA 20074451-T-TCA DYZ19 **
10008575-G-A 10170966-G-A **
22329346-C-T 20167460-C-T DYZ19 **
22280073-C-A 20118187-C-A DYZ19 ***
26148615-T-G 24002468-T-G P1_Y1 ***
13696283-G-A,C 11540607-G-A,C ***
58975667-C-T 56829520-C-T ***
28813318-T-G 26667171-T-G ***
28795943-A-T 26649796-A-T ***
27714328-CTTT-C 25568181-CTTT-C P1_Y2 15×T***
26398338-C-T 24252191-C-T P1_Y1 ***
26142904-T-G 23996757-T-G P1_Y1 ***
22275949-G-C 20114063-G-C DYZ19 ***
25818140-A-G 23671993-A-G P1_b3 ***
25461433-C-CTTTTT 23315286-C-CTTTTT P2_r2 26×T***
22309818-G-T 20147932-G-T DYZ19 ***
22304966-G-T 20143080-G-T DYZ19 ***
22234532-A-T 20072646-A-T DYZ19 ***
22289715-G-A 20127829-G-A DYZ19 ***
22241407-A-T 20079521-A-T DYZ19 ***
22260214-C-T 20098328-C-T DYZ19 ***
22269929-T-G 20108043-T-G DYZ19 ***
22430925-G-T 20269039-G-T DYZ19 ***
13862226-G-A 11741520-G-A ***
20048466-C-T 17936586-C-T P5_Prx ***
58974136-A-G 56827989-A-G ***
13820826-ATGGAT-A 11700120-ATGGAT-A ***
13748501-T-G 11592825-T-G ***
13455619-T-A 11299943-T-A ***
13455195-A-G 11299519-A-G ***
19411914-A-AAAAG,G 17300034-A-AAAAG,G 14×AAAG***
13804754-G-A 11684048-G-A ***
19815544-A-T 17703664-A-T P5_Prx ***
13804747-GAATTT-G 11684041-GAATTT-G ***
13676615-A-T 11520939-A-T ***
13451890-T-C 11296214-T-C ***
10024581-TC-T 10186972-TC-T ***
28795928-T-A 26649781-T-A ***
13464398-C-T 11308722-C-T ***
22232040-C-A 20070154-C-A BY10784 DYZ19 ***
26235428-C-T 24089281-C-T P1_Y1 ***
20033954-G-A 17922074-G-A P5_Prx ***
13728447-C-G 11572771-C-G ***
19792750-G-A 17680870-G-A P5_Prx ***
13858477-C-A,G 11737771-C-A,G ***
13851112-GAATCC-G 11730406-GAATCC-G ***
13850342-G-A 11729636-G-A ***
13728464-G-C 11572788-G-C ***
13728448-A-T 11572772-A-T ***
13728441-A-G 11572765-A-G ***
13447214-C-G 11291538-C-G ***
13728439-G-A 11572763-G-A ***
13728428-TGCAATC-T 11572752-TGCAATC-T ***
13728427-A-C 11572751-A-C ***
13648954-GAATGT-G 11493278-GAATGT-G ***
9179156-G-C 9341547-G-C ***
3131531-C-CTTCTCTTCT 3263490-C-CTTCTCTTCT ***
13451887-C-T 11296211-C-T ***
13141225-A-C,T 10630711-A-C,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.

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