McNair

BigY3: B1137

Tree Position

A0-T-YP2191 > P305[A1] > A1b > BT/A1b2 > M168/PF1416[CT] > M145/P205/PF144 > M96/PF1823 > P147 > P177 > 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
B1137
36565-T-G A+
16163593-A-T 14051713-A-T P8_Dst A+
20975524-G-A 18813638-G-A P4_Dst A+
21028963-A-G 18867077-A-G P4_Dst YA+
24588431-G-A 22442284-G-A P3_t2 A+
28806491-A-ATGGAGAGAAC 26660344-A-ATGGAGAGAAC A+
58977768-C-G 56831621-C-G A*
4466492-C-T 4598451-C-T A*
59018376-G-C 56872229-G-C A*
28806582-T-A 26660435-T-A A*
28817732-T-C 26671585-T-C A*
13451271-C-A 11295595-C-A A*
28817854-G-A 26671707-G-A A*
28785076-G-T 26638929-G-T A*
28816789-T-C 26670642-T-C A*
56829598-T-C A*
28816693-G-A 26670546-G-A A*
16112272-T-A 14000392-T-A P8_Prx A*
56834045-A-T A*
4134271-G-C 4266230-G-C A*
4386594-A-G 4518553-A-G A*
4674577-A-C 4806536-A-C A*
6170945-C-T 6302904-C-T IR3_Dst A*
6243003-C-T 6374962-C-T IR3_Dst A*
6250156-T-C 6382115-T-C FTB47384 IR3_Dst A*
9603139-A-G 9765530-A-G IR3_Prx A*
13478002-C-G 11322326-C-G A*
13478011-C-T 11322335-C-T A*
13867300-C-A 11746594-C-A A*
18305412-T-C 16193532-T-C P6_Prx A*
18344737-C-T 16232857-C-T P6_Prx A*
18344825-A-G 16232945-A-G P6_Prx A*
19614509-G-A 17502629-G-A P5_Prx YA*
19829340-C-G 17717460-C-G P5_Prx A*
19833229-C-G 17721349-C-G P5_Prx A*
19858035-G-A 17746155-G-A P5_Prx A*
20008064-T-C 17896184-T-C P5_Prx A*
20346549-G-C 18184663-G-C P5_Dst A*
24290285-C-T 22144138-C-T P3_t1 A*
24297134-C-T 22150987-C-T P3_t1 A*
24870891-C-A 22724744-C-A FT460999 IR1_R A*
25967757-T-C 23821610-T-C BY49378 P1_Y1 A*
26357828-C-T 24211681-C-T P1_Y1 A*
26398122-G-A 24251975-G-A P1_Y1 A*
28806532-T-C 26660385-T-C A*
28806536-A-G 26660389-A-G A*
28806540-T-A 26660393-T-A A*
28806543-A-G 26660396-A-G A*
28817644-G-C 26671497-G-C A*
56831735-C-A A*
56831835-T-C A*
56834213-C-T A*
56837086-T-C A*
10980264-C-T FT439020 +
10953176-C-G FT437979 +
2989556-C-G 3121515-C-G FT84261 +
3514815-C-A 3646774-C-A FT84338 +
4036765-C-A 4168724-C-A FT84426 +
4814414-C-A 4946373-C-A FT84547 +
5322880-G-A 5454839-G-A FT84638 +
5513367-G-A 5645326-G-A FT84666 +
5618619-A-G 5750578-A-G FT84682 +
6362928-A-T 6494887-A-T BY164194 +
6520782-T-G 6652741-T-G FT84780 +
7761963-CTTTG-C 7893922-CTTTG-C +
7884630-T-A 8016589-T-A BY164292 YY+
8660258-C-T 8792217-C-T FT8775 YY+
8696740-G-A 8828699-G-A BY164373 YY+
10067290-G-A 10229681-G-A FT427178 +
10934882-C-T FT437182 +
13216401-C-T 11060725-C-T FT92302 +
13692592-C-A 11536916-C-A +
11660082-G-A BY41374 +
14205526-T-C 12084820-T-C BY163544 YY+
15052012-T-C 12940103-T-C BY163606 YY+
15061451-A-G 12949543-A-G BY163607 YY+
15113756-G-A 13001843-G-A FT84968 YY+
15327161-G-A 13215279-G-A BY163621 YY+
15797465-G-C 13685585-G-C FT84997 Y+
16775947-A-G 14664067-A-G FT85046 YY+
17345838-G-T 15233958-G-T BY163760 YY+
17786009-G-C 15674129-G-C FT85107 Y+
18090988-A-T 15979108-A-T BY163814 YY+
18224931-T-C 16113051-T-C BY163824 Y+
18232479-G-A 16120599-G-A Y+
18254264-T-C 16142384-T-C BY163829 Y+
18262756-T-C 16150876-T-C BY163831 +
18799550-C-T 16687670-C-T FT85145 Y+
18903218-T-C 16791338-T-C BY163865 YY+
18954570-AAAT-A 16842690-AAAT-A +
20707583-A-T 18545697-A-T FT452796 P4_Prx +
21161214-G-C 18999328-G-C BY163936 YY+
21364186-A-G 19202300-A-G BY163957 YY+
21655916-GA-G 19494030-GA-G +
21740413-C-T 19578527-C-T BY163987 YY+
21946101-C-G 19784215-C-G BY164004 YY+
22437171-G-T 20275285-G-T BY163477 DYZ19 +
22521530-G-A 20359644-G-A BY164025 Y+
22759291-A-G 20597405-A-G BY164041 YY+
24370425-G-A 22224278-G-A +
28625407-T-C 26479260-T-C FT85308 +
18221-G-A +
8555979-T-TTTTTG 8687938-T-TTTTTG S190 8×TTTTG*
3793409-T-C 3925368-T-C *
4371897-G-C 4503856-G-C *
4559826-C-T 4691785-C-T *
4629046-A-G 4761005-A-G *
4796204-C-T 4928163-C-T *
5841052-C-G 5973011-C-G *
58968361-T-C 56822214-T-C *
58970069-T-G 56823922-T-G *
58990073-C-A 56843926-C-A *
58993630-C-T 56847483-C-T *
58995875-C-T 56849728-C-T *
59021159-C-T 56875012-C-T *
56850971-C-G *
14879536-C-CTGTG 12767606-C-CTGTG 16×TG*
13452462-C-T 11296786-C-T *
2708411-CGAGAGAGAGAGA-C 2840370-CGAGAGAGAGAGA-C 23×GA*
56851491-T-G *
13462137-C-A 11306461-C-A *
11033540-A-ACCATT *
13450111-CCACCCCATCCCATCCCATTCTATTCCATTC-C,CCATTCCATTCCATGCCATTCCATTCCATTT 11294435-CCACCCCATCCCATCCCATTCTATTCCATTC-C,CCATTCCATTCCATGCCATTCCATTCCATTT *
3928680-T-C 4060639-T-C *
4472832-G-A 4604791-G-A *
4647564-C-T 4779523-C-T *
4650418-G-T 4782377-G-T *
4692751-T-C 4824710-T-C *
4792167-G-A 4924126-G-A *
5085081-CCT-C 5217040-CCT-C *
5841085-C-G 5973044-C-G *
6173736-A-C 6305695-A-C BY164191 IR3_Dst *
6434685-TAAGA-T 6566644-TAAGA-T *
17275753-AAAGAA-A,AAAGGGAAGGG 15163873-AAAGAA-A,AAAGGGAAGGG *
20936596-T-A 18774710-T-A P4_Dst *
56823982-T-A *
56830228-CA-T *
56830441-G-A *
56833843-CCCACTCCACT-C 4×CCACT*
19013219-C-T 16901339-C-T **
22475462-G-T 20313576-G-T BY223356 DYZ19 **
13692749-C-A 11537073-C-A **
13557010-C-A 11401334-C-A **
24673206-T-G 22527059-T-G P3_b2 **
4764741-GCA-G 4896700-GCA-G **
5770905-T-G 5902864-T-G **
6603358-T-C 6735317-T-C **
10081890-A-G 10244281-A-G **
14213582-A-G 12092876-A-G **
12372479-T-C FT41608 **
14815262-G-A 12703333-G-A **
15893562-T-C 13781682-T-C **
17735221-T-C 15623341-T-C **
18007575-T-C 15895695-T-C P7_Gap **
18201976-TTTAA-T 16090096-TTTAA-T 4×TTAA**
18487617-A-T 16375737-A-T P6_Dst **
18487622-C-A 16375742-C-A P6_Dst **
19387616-T-C 17275736-T-C **
19950179-TATA-T 17838299-TATA-T P5_Prx **
21738542-A-G 19576656-A-G **
22267101-G-A 20105215-G-A BY214829 DYZ19 **
22465269-G-A 20303383-G-A DYZ19 **
22471369-C-T 20309483-C-T BY21791 DYZ19 **
22526394-A-G 20364508-A-G **
25727913-C-CAT 23581766-C-CAT P1_b3 **
25995382-G-A 23849235-G-A P1_Y1 **
26138735-G-A 23992588-G-A P1_Y1 **
26324270-GTTTT-G 24178123-GTTTT-G P1_Y1 20×T**
17737-T-A **
59030478-A-AAAACAAAAAAC 56884331-A-AAAACAAAAAAC 6×AAAC***
59011559-C-T 56865412-C-T ***
13467187-C-T 11311511-C-T ***
4118723-C-CAA 4250682-C-CAA 13×A***
8085516-CTTTT-C 8217475-CTTTT-C 19×T***
16768601-CTTT-C,CT 14656721-CTTT-C,CT 17×T***
13461081-G-A,T 11305405-G-A,T ***
13461057-A-G 11305381-A-G ***
3220600-GTT-G 3352559-GTT-G 14×T***
10987627-G-T ***
16823952-TA-T,TAA 14712072-TA-T,TAA 17×A***
23034293-CT-C,CTT 20872407-CT-C,CTT 15×T***
10816518-G-GTTCCATTCCATTCCA ***
13467192-G-C 11311516-G-C ***
22127975-CTTTTTTT-C 19966089-CTTTTTTT-C 20×T***
13467213-C-G 11311537-C-G ***
13467236-C-T 11311560-C-T ***
14753642-GA-G 12641711-GA-G 10×A***
13708936-A-G,T 11553260-A-G,T ***
3301288-C-CACAT 3433247-C-CACAT ***
6929132-CTT-C,CT 7061091-CTT-C,CT 26×T***
3079722-TAA-T,TA 3211681-TAA-T,TA 14×A***
4517043-G-T 4649002-G-T ***
3703516-A-C 3835475-A-C ***
4370624-CACACACACAG-C,CACACACACACAG 4502583-CACACACACAG-C,CACACACACACAG ***
4697512-A-G 4829471-A-G ***
5205635-A-ATT 5337594-A-ATT 14×T***
5211584-A-G 5343543-A-G BY2823FT129980 ***
7643536-AGGAAAGGAAGGGAAGGGAAG-A,AGGAAGGGAAGGGAAGGGAAG 7775495-AGGAAAGGAAGGGAAGGGAAG-A,AGGAAGGGAAGGGAAGGGAAG ***
8907673-A-ATGTG,ATGTGTG 9039632-A-ATGTG,ATGTGTG 18×TG***
10664658-GCCACTCCACTCCATT-G,GCCACTCCACTCCATG ***
10889768-TCC-T ***
13475780-T-G 11320104-T-G ***
13476677-G-T 11321001-G-T ***
13477313-C-T 11321637-C-T ***
13478046-C-A 11322370-C-A ***
13478120-A-T 11322444-A-T ***
14222654-T-A 12101948-T-A ***
14289026-T-A 12168320-T-A ***
14392931-AT-A 12272227-AT-A ***
14682807-A-C 12570873-A-C ***
15477863-C-T 13365983-C-T ***
16908409-A-G 14796529-A-G ***
16938218-C-CT,CTT 14826338-C-CT,CTT 19×T***
17518942-G-A 15407062-G-A ***
18124427-A-AAAGG 16012547-A-AAAGG ***
18232289-G-A 16120409-G-A ***
18940817-G-A 16828937-G-A ***
18940829-G-A 16828949-G-A ***
19251061-A-AT 17139181-A-AT ***
21394011-A-T 19232125-A-T ***
22269738-T-C 20107852-T-C DYZ19 ***
23194818-T-C 21032932-T-C ***

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.