Reed

BigY3: 110236
MDKA Birth: United States > Massachusetts 1770

Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z258 > Z367/S255 > Z34/S368 > Z33/S212 > BY164497 > BY3604 > Z256 > Z275 > FT316723 > FT369318 > BY200627

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
110236
3062015-T-A 3193974-T-A A*
4237208-C-G 4369167-C-G A*
19933043-C-T 17821163-C-T BY35830 P5_Prx A*
10952227-T-C A*
3248606-A-G 3380565-A-G A*
56836776-C-T A*
19683284-G-A 17571404-G-A P5_Prx A*
24298612-T-G 22152465-T-G P3_t1 A*
6167417-A-G 6299376-A-G IR3_Dst A*
19885222-T-C 17773342-T-C P5_Prx A*
24250616-T-C 22104469-T-C P3_b1 A*
25887777-C-G 23741630-C-G P1_Y1 A*
26061528-T-C 23915381-T-C P1_Y1 A*
56834061-C-A A*
19265333-G-A 17153453-G-A FGC35410 YY+
23589820-G-A 21427934-G-A FT315024 YY+
28707307-C-T 26561160-C-T FT369689 Y+
13236871-C-T 11081195-C-T BY160561BY84830 +
14746708-G-A 12634777-G-A FT146520 YY+
19700804-GT-G 17588924-GT-G P5_Prx 15×T+
2955476-C-T 3087435-C-T FT368127 +
3608160-C-T 3740119-C-T FT368212 +
4562010-T-C 4693969-T-C FT368309 +
4823094-C-G 4955053-C-G FT368334 +
6356463-G-T 6488422-G-T FT368465 +
7410814-C-T 7542773-C-T FT368559 YY+
7997583-G-C 8129542-G-C FT368613 YY+
9511743-C-G 9674134-C-G FT368760 +
9778559-G-A 9940950-G-A FT368768 Y+
14098830-T-C 11978124-T-C FT368835 YY+
16314437-A-G 14202557-A-G FT369054 YY+
16478975-A-G 14367095-A-G FT369079 YY+
17168486-A-G 15056606-A-G FT369154 YY+
19277618-C-A 17165738-C-A FT369385 YY+
19338844-A-G 17226964-A-G FT369392 YY+
20822500-T-A 18660614-T-A FT370092 P4_Gap +
21303471-T-C 19141585-T-C FT369443 YY+
21316382-T-C 19154496-T-C FT369445 YY+
21694896-G-A 19533010-G-A YY+
21928958-A-G 19767072-A-G FT369491 YY+
22512588-G-A 20350702-G-A FT460802 DYZ19 +
23535730-G-A 21373844-G-A BY22149 YY+
23742918-G-A 21581032-G-A FT369619 +
23761776-C-CCA 21599890-C-CCA 12×CA*
6001222-A-G 6133181-A-G *
10677341-C-T *
22233583-C-G 20071697-C-G DYZ19 *
21515862-CA-C 19353976-CA-C 28×A**
3411690-CAA-C 3543649-CAA-C 30×A**
28076495-TTTCC-T 25930348-TTTCC-T P1_Y2 7×TTCC**
28076530-TCTTTCTTTCTTTC-T 25930383-TCTTTCTTTCTTTC-T P1_Y2 **
20597157-T-TTTTG 18435271-T-TTTTG P5_Dst 4×TTTG**
23082659-C-CT 20920773-C-CT 8×T**
22955937-G-T 20794051-G-T **
15883973-G-GT 13772093-G-GT 10×T**
18132772-AT-A 16020892-AT-A 9×T**
5211436-A-G 5343395-A-G **
6449668-C-G 6581627-C-G FTB47396 **
7094977-T-C 7226936-T-C **
7116314-T-C 7248273-T-C **
9492934-C-G 9655325-C-G **
9913890-A-G 10076281-A-G **
14251266-T-C 12130560-T-C **
15081700-T-G 12969790-T-G **
17855110-A-C 15743230-A-C **
18121293-A-G 16009413-A-G **
18630669-T-C 16518789-T-C **
19498946-C-T 17387066-C-T **
20693148-A-G 18531262-A-G P4_Prx **
20801604-T-C 18639718-T-C P4_Prx **
21262163-G-GT 19100277-G-GT **
22983589-C-A 20821703-C-A **
23009686-C-A 20847800-C-A **
23231061-T-C 21069175-T-C **
23333140-G-A 21171254-G-A **
27761297-A-ACAT 25615150-A-ACAT P1_Y2 **
28619206-C-T 26473059-C-T **
17292636-C-CT 15180756-C-CT 10×T***
13478067-G-A 11322391-G-A ***
22293463-T-G 20131577-T-G PF1849 DYZ19 ***
22293468-G-A 20131582-G-A BY26475 DYZ19 ***
3179250-GTC-G 3311209-GTC-G ***
16740678-A-AT 14628798-A-AT 9×T***
4420418-CTT-C 4552377-CTT-C 13×T***
10947389-A-T ***
15957809-TTTA-T 13845929-TTTA-T ***
13842711-C-G 11722005-C-G ***
2686435-CA-C,CAA 2818394-CA-C,CAA 13×A***
28628234-CTT-C 26482087-CTT-C 13×T***
23522599-G-A 21360713-G-A ***
8403272-CAAAAAAA-C 8535231-CAAAAAAA-C 28×A***
28500806-CTT-C,CTTT 26354659-CTT-C,CTTT 18×T***
13152819-TG-T,TGG 13×G***
13470902-C-G 11315226-C-G ***
4669265-ATT-A,AT 4801224-ATT-A,AT 15×T***
4773481-C-CTTTT 4905440-C-CTTTT 25×T***
7002534-A-T 7134493-A-T ***
7569550-T-C 7701509-T-C ***
7753365-T-C 7885324-T-C ***
9173339-A-G 9335730-A-G ***
13862171-TAATGG-T 11741465-TAATGG-T ***
14604590-CT-C,CTTT 12492792-CT-C,CTTT 21×T***
14738809-A-G 12626877-A-G ***
15957796-T-A 13845916-T-A ***
16687059-A-G 14575179-A-G ***
17229273-C-A 15117393-C-A ***
17387231-T-C 15275351-T-C ***
17648536-ATTT-A,ATTTTT 15536656-ATTT-A,ATTTTT 22×T***
19326665-C-G 17214785-C-G ***
22160925-T-C 19999039-T-C ***
22430915-A-G 20269029-A-G DYZ19 ***
22642187-A-G 20480301-A-G ***
23537403-A-G 21375517-A-G ***
23831155-T-C 21669269-T-C ***
26262520-T-A 24116373-T-A P1_Y1 ***
28763064-A-T 26616917-A-T ***
56828936-TTCCATTCCATTCCA-T,TTAGATTCTATTCCATTCCAT ***
56828953-TC-T,TGTTAC 4×CATTC***

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.