Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > FGC5494 > FGC5561 > Z16503 > Z16502 > A7537

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
166617
BigY3
166617
Manual
Edits
24585344-C-G 22439197-C-G P3_t2 A+
24293374-G-C 22147227-G-C M222Z16323 P3_t1 A+
28402308-A-G 26256161-A-G P1_gr2 A*
25576437-A-G 23430290-A-G P1_gr1 A*
26120269-C-T 23974122-C-T BY226664 P1_Y1 A*
25984302-A-C 23838155-A-C BY11724BY11725 P1_Y1 A*
18304450-G-A 16192570-G-A P6_Prx A*
25986896-A-G 23840749-A-G P1_Y1 A*
22290995-T-G 20129109-T-G DYZ19 A*
18504652-C-T 16392772-C-T FGC59197 P6_Dst A*
19571589-C-G 17459709-C-G P5_Prx YA*
19830211-A-G 17718331-A-G ZZ81_1 P5_Prx A*
6585757-G-A 6717716-G-A A*
25560606-T-C 23414459-T-C P1_gr1 A*
26017011-C-T 23870864-C-T P1_Y1 A*
26394629-C-CT 24248482-C-CT P1_Y1 8×TA*
18310695-A-C 16198815-A-C P6_Prx A*
18440413-T-TAC 16328533-T-TAC P6_Dst 17×ACA*
27945391-G-A 25799244-G-A P1_Y2 A*
25618948-T-G 23472801-T-G P1_gr1 A*
20510821-A-G 18348935-A-G P5_Dst A*
19592783-T-C 17480903-T-C P5_Prx YA*
20510818-T-C 18348932-T-C P5_Dst A*
18988316-G-A 16876436-G-A M222Z2982 S648 AM01910 Y+
20816920-G-A 18655034-G-A Y19870Y19870 P4_Gap +
17669040-A-G 15557160-A-G A259A259 YY+
13444283-T-C 11288607-T-C M222FGC33465 +
22861537-G-A 20699651-G-A Y19870A260 YY+
5004912-A-T 5136871-A-T Z2956Z2958 +
3331464-T-A 3463423-T-A M222FGC435 +
4915019-C-A 5046978-C-A DF49/S474Y2599 FGC436 +
13953551-C-T 11832845-C-T M222S634 Z2967 AM01901 Y+
3045441-T-A 3177400-T-A Z2956Y2597 FGC439 +
3090830-C-G 3222789-C-G M222FGC7512 +
2794472-C-G 2926431-C-G BY18114 YY+
7206305-C-A 7338264-C-A A10525A10525 YY+
9120959-C-T A18726A18726 +
22057062-T-C 19895176-T-C FT73500 Y+
18097801-C-T 15985921-C-T FT73435 YY+
15920270-TC-T 13808390-TC-T +
13243459-C-T 11087783-C-T +
11032691-TTCCAC-T +
10874487-T-C +
5948313-G-A 6080272-G-A FT18188 +
16938349-T-G 14826469-T-G FT73413 YY+
7243731-C-T 7375690-C-T M222Z2960 AM01917 YY+
10748233-A-C FGC78684 +
19231664-T-C 17119784-T-C YY+
17873273-C-T 15761393-C-T YY+
17137788-G-A 15025908-G-A YY+
16545347-G-A 14433467-G-A YY+
15547613-C-G 13435733-C-G YY+
9861500-A-G 10023891-A-G BY18151 YY+
4293715-G-A 4425674-G-A Z2956Z2957 +
22735599-G-A 20573713-G-A DF49/S474DF49 S474 AM01922 YY+
23581931-A-C 21420045-A-C M222S6152 Z2990 YY+
8909149-A-C 9041108-A-C M222S6155 Z2965 +
15399507-A-C 13287627-A-C M222S642 Z2974 AM01907 Y+
15344019-A-C 13232138-A-C M222S641 Z2973 AM01906 YY+
14902414-G-A 12790481-G-A M222M222 PAGES00084 Page84 YY+
23480728-A-G 21318842-A-G M222S652 Z2989 AM01913 YY+
14418666-C-A 12297941-C-A DF106DF106 S658 Y2841 FGC4100 YY+
14372339-A-G 12251635-A-G M222Z2971 AM01904 YY+
15731346-T-C 13619466-T-C M222Z2975 S643 AM01908 YY+
15994422-C-G 13882542-C-G Z2976S476 Z2976 AM01919 YY+
16419368-C-T 14307488-C-T Z2956S645 Z2977 AM01920 YY+
17774409-G-A 15662529-G-A DF23DF23 S193 YY+
19391822-T-G 17279942-T-G Z2976Z2983 S6146 S475 AM01921 YY+
14365440-G-C 12244735-G-C M222S637 Z2970 AM01903 YY+
7717685-T-TTTCCTTCC 7849644-T-TTTCCTTCC 13×TTCC+
14010329-A-G 11889623-A-G M222S635 Z2968 AM01902 YY+
22540855-A-T 20378969-A-T DF105DF109 S660 Y2845 FGC4101 Y+
15172051-G-A 13060137-G-A M222S640 Z2972 AM01905 YY+
8157356-A-G 8289315-A-G M222FGC449 Y2596 S7072 YY+
23959290-C-T 21813143-C-T M222S6141 Z2991 Y+
9574554-A-C 9736945-A-C Z2956Y2601 IR3_Prx +
7855252-C-T 7987211-C-T Z2961Z2961 YY+
8343779-A-G 8475738-A-G M222Z2964 YY+
23295679-C-T 21133793-C-T M222S651 Z2988 AM01912 YY+
23856771-A-C 21694885-A-C Z2956S6149 Y2602 FGC438 Y+
2805834-C-T 2937793-C-T DF104DF104 S661 Y2842 FGC4099 YY+
8180494-T-C 8312453-T-C M222Z2962 YY+
8224850-C-A 8356809-C-A M222Z2963 YY+
2822914-T-G 2954873-T-G Z2956Z2956 AM01923 YY+
56832915-ACTCCATTCCACTCCA-A,ACTCCATTCCACTCC *
22281021-T-G 20119135-T-G M222BY24417 DYZ19 *
16838962-A-AAAAG 14727082-A-AAAAG 5×AAAG*
3427557-A-G 3559516-A-G FGC81616 *
13489107-C-T 11333431-C-T *
27842167-G-A 25696020-G-A BY28854 P1_Y2 *
3991966-ACA-A,ACT 4123925-ACA-A,ACT *
24244723-G-T 22098576-G-T P3_b1 **
58997410-T-G 56851263-T-G M222FGC33464 **
10081968-C-G 10244359-C-G FT44712 **
5288847-T-C 5420806-T-C Z2956Y2600 FGC437 **
8981887-G-A 9144278-G-A FGC16004 BY13672 **
17997565-T-C 15885685-T-C Z2980Z2980 S6154 P7_Gap **
20771797-G-T 18609911-G-T P4_Prx **
4634558-CAA-C 4766517-CAA-C 28×A**
10653240-ACCATTCCATT-A **
22448882-C-T 20286996-C-T DYZ19 **
13455915-A-T 11300239-A-T **
21009475-T-TGA 18847589-T-TGA P4_Dst **
11002150-A-G **
6268766-AC-A 6400725-AC-A IR3_Dst **
21422276-G-T 19260390-G-T **
22448873-T-C 20286987-T-C DYZ19 **
24289891-A-T 22143744-A-T P3_t1 **
19832285-A-G 17720405-A-G P5_Prx **
6175172-C-A 6307131-C-A IR3_Dst **
3999821-GTATATATATA-G 4131780-GTATATATATA-G 17×TA**
13455913-C-A 11300237-C-A **
13455909-C-A 11300233-C-A **
9364686-G-A 9527077-G-A **
25305239-A-T 23159092-A-T P2_r1 **
26012967-G-T 23866820-G-T P1_Y1 **
20752685-C-A 18590799-C-A P4_Prx **
7474374-AAGAG-A,AAG 7606333-AAGAG-A,AAG IR1_L 21×AG***
18577306-G-A 16465426-G-A ***
11006381-TTCCAC-T ***
7164467-CAAAA-C,CAAA 7296426-CAAAA-C,CAAA 24×A***
7053358-AAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-A,AAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 7185317-AAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-A,AAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 17×AAAG***
13489112-G-T 11333436-G-T ***
19318178-CTTTTT-C 17206298-CTTTTT-C 28×T***
10026480-A-T 10188871-A-T ***
24142357-G-A 21996210-G-A P3_b1 ***
13489136-C-A 11333460-C-A ***
13810068-CGTTTGTAATG-C 11689362-CGTTTGTAATG-C ***
22449289-T-G 20287403-T-G DYZ19 ***
22258359-T-G 20096473-T-G A3981 DYZ19 ***
16108627-C-T 13996747-C-T P8_Prx ***
13865724-G-A 11745018-G-A ***
13855605-G-C 11734899-G-C ***
13850220-T-A 11729514-T-A ***
13838607-A-G 11717901-A-G ***
13836376-A-G 11715670-A-G ***
13832987-A-G 11712281-A-G ***
13828187-G-A 11707481-G-A ***
13815585-G-A 11694879-G-A ***
13810055-A-T 11689349-A-T ***
22449418-A-T 20287532-A-T DYZ19 ***
13809984-G-T 11689278-G-T FT57720 ***
13809974-G-T 11689268-G-T ***
13805303-A-G 11684597-A-G ***
13801855-A-G 11681149-A-G ***
13676749-G-C 11521073-G-C ***
13651448-G-C 11495772-G-C ***
13480543-C-A 11324867-C-A ***
13472278-C-T 11316602-C-T ***
13472273-T-A 11316597-T-A ***
13143026-A-C 10632512-A-C ***
13142948-G-GCATTCCATTCCATTC 10632434-G-GCATTCCATTCCATTC 11×CATTC***
22449335-T-C 20287449-T-C DYZ19 ***
22449420-A-T 20287534-A-T DYZ19 ***
13455771-CTCAAGTTGATTCAAGTCCAT-C,T 11300095-CTCAAGTTGATTCAAGTCCAT-C,T ***
7211969-A-C 7343928-A-C ***
13138458-C-T 10627944-C-T ***
13652250-G-A 11496574-G-A ***
22435748-G-A 20273862-G-A DYZ19 ***
16108625-A-G 13996745-A-G P8_Prx ***
58975094-TCCA-T 56828947-TCCA-T ***
13472522-A-C,G 11316846-A-C,G ***
10036746-C-T 10199137-C-T ***
13452766-A-C 11297090-A-C ***
13854237-T-G 11733531-T-G ***
13651397-TGGAAC-T 11495721-TGGAAC-T ***
6180054-TTTG-T 6312013-TTTG-T IR3_Dst 7×TTG***
7211973-A-C 7343932-A-C ***
22449423-G-T 20287537-G-T DYZ19 ***
9300402-G-C 9462793-G-C ***
9987812-G-T 10150203-G-T ***
58982279-G-A,T 56836132-G-A,T ***
58844548-T-C 56746323-A-G ***
58819474-A-T 56771397-T-A ***
58819458-C-T 56771413-G-A ***
58819418-T-G 56771453-A-C ***
13823328-C-G 11702622-C-G ***
28800219-A-G 26654072-A-G ***
28786596-A-G 26640449-A-G ***
28785629-A-G 26639482-A-G ***
22456709-T-A 20294823-T-A DYZ19 ***
28800234-GTGGAAAGGAA-G 26654087-GTGGAAAGGAA-G ***

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.

Mutation Notes:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual6734646-C-G6866605-C-G17G + 4 additional reads not aligned properly.
Manual17515249-C-G15403369-C-G8G

Haplotype Progression

The data below reveals the progression of changes in the haplotype. The bottom row is the haplotype for this man and above him are the inferred ancestral haplotypes for various upstream blocks. These inferred haplotypes are very much a work in progress, and any suggested modifications are appreciated. I think we can use our vast collection of haplotype data to refine these haplotypes. Mutations made from each upstream block are shown in sequence. The cell color is determined by the block in which the mutation took place.

DYS393
DYS390
DYS19
DYS391
DYS385
DYS426
DYS388
DYS439
DYS389i
DYS392
DYS389ii
DYS458
DYS459
DYS455
DYS454
DYS447
DYS437
DYS448
DYS449
DYS464
DYS460
Y-GATA-H4
YCAII
DYS456
DYS607
DYS576
DYS570
CDY
DYS442
DYS438
DYS531
DYS578
DYF395S1
DYS590
DYS537
DYS641
DYS472
DYF406S1
DYS511
DYS425
DYS413
DYS557
DYS594
DYS436
DYS490
DYS534
DYS450
DYS444
DYS481
DYS520
DYS446
DYS617
DYS568
DYS487
DYS572
DYS640
DYS492
DYS565
DYS710
DYS485
DYS632
DYS495
DYS540
DYS714
DYS716
DYS717
DYS505
DYS556
DYS549
DYS589
DYS522
DYS494
DYS533
DYS636
DYS575
DYS638
DYS462
DYS452
DYS445
Y-GATA-A10
DYS463
DYS441
Y-GGAAT-1B07
DYS525
DYS712
DYS593
DYS650
DYS532
DYS715
DYS504
DYS513
DYS561
DYS552
DYS726
DYS635
DYS587
DYS643
DYS497
DYS510
DYS434
DYS461
DYS435
P312/S1161324141111-14121212131329179-1011112515192915-15-17-17111119-231615181736-38121211915-1681010810101223-231610121215812222013121113111112123315916122626191211131210912121011113012132413101020151913241712152412231810141791211
L21/S1451324141111-14121212131329179-1011112515192915-15-17-17111119-231615181736-38121211915-1681010810101223-231610121215812222013121113111112123515916122526191211131211912121011113012132413101020151913241712152412231810141791211
Wiegand1324151111-14121212131329179-1011112516202816-16-17-17121117-231616181736-39121211915-1681010810101223-23161012121681222221312111311111212351591612252619131113121191212101111301213241310102015191425161215241223189141791211

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 1666171077289578075067888537
Kit: 1666171482627593192078318292
Used in age calculations1482627593192078318292
Counts of SNPs4338
Variant counts last updated 2019-09-27 03:33:53.



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