Simmons

BigY2: 780227

Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z251/S470 > S11556 > BY82274 > Y128338

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 STRBigY2
780227
13687857-G-A 11532181-G-A A*
20747542-C-T 18585656-C-T P4_Prx A*
25885606-G-T 23739459-G-T P1_Y1 A*
26181022-T-C 24034875-T-C P1_Y1 A*
8402989-G-A 8534948-G-A BY12313BY12322 YY+
14022377-C-A 11901671-C-A FGC32963 YY+
17093993-G-A 14982113-G-A Y129451 YY+
2800649-T-C 2932608-T-C Y128091 YY+
6844582-A-G 6976541-A-G Y128075 YY+
7083578-G-A 7215537-G-A Y128448 YY+
7188785-G-A 7320744-G-A BY63758 YY+
8070348-G-C 8202307-G-C Y128045 YY+
8097375-C-T 8229334-C-T Y128938 YY+
8270888-A-T 8402847-A-T Y129917 YY+
8450468-G-C 8582427-G-C Y129559 YY+
8454577-G-T 8586536-G-T Y129514 YY+
8465433-C-T 8597392-C-T Y128158 YY+
8497974-T-A 8629933-T-A BY73425 YY+
9087221-T-A 9249612-T-A Y128233 Y+
9154496-G-C 9316887-G-C Y128772 Y+
9422420-C-CA 9584811-C-CA +
10025678-G-A 10188069-G-A BY83126 Y+
14503669-C-T 12391874-C-T Y129006 YY+
15032029-T-G 12920117-T-G BY99259 YY+
15730111-T-G 13618231-T-G Y128651 YY+
15983073-G-A 13871193-G-A Y130430 YY+
16017838-T-C 13905958-T-C Y128224 Y+
16017844-T-C 13905964-T-C Y128496 Y+
16560999-C-A 14449119-C-A Y128925 YY+
17395119-G-A 15283239-G-A Y53209 YY+
18881007-T-C 16769127-T-C Y130305 YY+
19162322-G-A 17050442-G-A F23396 YY+
19511930-A-G 17400050-A-G Y129459 YY+
19563806-G-A 17451926-G-A Y130234 Y+
21456462-G-T 19294576-G-T Y129264 YY+
21835705-G-T 19673819-G-T Y128752 Y8×T+
21918972-A-G 19757086-A-G Y128128 YY+
22067075-G-A 19905189-G-A Y129920 YY+
22660091-C-T 20498205-C-T Y78447 YY+
23163053-T-C 21001167-T-C Y128301 Y+
24454540-T-C 22308393-T-C Y128746 Y+
22422622-G-T 20260736-G-T DYZ19 *
22254541-G-A 20092655-G-A DYZ19 *
22300388-G-A 20138502-G-A DYZ19 *
23437953-ATA-A,ATG 21276067-ATA-A,ATG *
3545949-T-C 3677908-T-C FTA2849 **
5186421-G-A 5318380-G-A FT107030 **
18972172-TAATAAATA-T 16860292-TAATAAATA-T 9×AATA**
13457747-A-G 11302071-A-G **
22428377-C-A 20266491-C-A DYZ19 **
13698883-G-T 11543207-G-T **
10764644-C-T **
5367687-C-A 5499646-C-A **
10683085-G-T **
10683107-C-G **
14614589-C-A 12502787-C-A **
56844083-G-T **
17318340-C-A 15206460-C-A **
17043026-C-A 14931146-C-A **
28781514-C-A 26635367-C-A **
6475356-C-A 6607315-C-A **
10885139-C-T **
10782833-G-T **
10858512-T-C **
10954378-C-A **
6682171-A-C 6814130-A-C **
10984028-C-A **
11026170-A-T FT440025 **
13880755-C-A 11760049-C-A FT168254 **
6682213-T-G 6814172-T-G **
7238193-C-A 7370152-C-A **
22240976-C-A 20079090-C-A DYZ19 **
23831306-G-A 21669420-G-A **
24577935-T-A 22431788-T-A P3_t2 **
13726021-GACTGGAATGGA-G 11570345-GACTGGAATGGA-G **
13726034-T-TA 11570358-T-TA **
10664837-C-A **
9416727-C-A 9579118-C-A **
5603789-C-A 5735748-C-A **
4703763-C-A 4835722-C-A **
6233730-A-ACT 6365689-A-ACT IR3_Dst **
13487754-CAA-C 11332078-CAA-C **
10930035-A-C **
7536392-C-A 7668351-C-A **
3620738-C-A 3752697-C-A **
3804509-C-A 3936468-C-A **
18701785-C-A 16589905-C-A **
14557559-G-T 12445760-G-T **
21367418-C-A 19205532-C-A **
4466804-C-A 4598763-C-A **
11028278-C-T **
3252378-C-A 3384337-C-A **
10800710-C-T **
9945436-G-T 10107827-G-T **
6714567-C-A 6846526-C-A **
10792808-T-A **
6293872-T-G 6425831-T-G IR3_Dst **
11672974-A-C **
10888303-A-G **
10888314-C-T **
10888321-C-T **
10888328-G-A FGC82224 **
13566671-G-T 11410995-G-T **
10669016-C-A **
4244640-C-A 4376599-C-A **
10945436-T-C **
22660887-C-A 20499001-C-A **
6868-C-A **
10895982-C-A **
9822822-A-G 9985213-A-G **
10989112-C-G **
10844240-T-G FT65926 **
13456657-G-A 11300981-G-A **
19911450-A-C 17799570-A-C P5_Prx **
19293589-C-A 17181709-C-A **
10005935-C-A 10168326-C-A **
7169934-C-A 7301893-C-A **
18465495-AGC-A 16353615-AGC-A P6_Dst **
11030616-G-C **
6790407-C-A 6922366-C-A **
14981761-C-A 12869837-C-A **
15785915-C-A 13674035-C-A **
10751743-T-G **
17093651-C-A 14981771-C-A **
14008808-T-G 11888102-T-G **
10981722-G-T **
14779583-A-G 12667653-A-G **
10821922-CAT-C **
28798391-C-A 26652244-C-A **
15788046-C-A 13676166-C-A **
15364695-T-G 13252815-T-G **
10693185-C-A **
10765016-TATTCC-T **
4995482-C-A 5127441-C-A **
10973270-C-A **
16432786-G-C 14320906-G-C **
7100560-C-A 7232519-C-A **
4293939-AT-A 4425898-AT-A 9×T**
2651414-C-A 2783373-C-A **
2651741-C-A 2783700-C-A **
2812851-C-T 2944810-C-T **
2852622-C-A 2984581-C-A **
3016413-C-A 3148372-C-A **
3139469-G-T 3271428-G-T FTA26324 **
3145024-CA-C 3276983-CA-C **
3158503-G-A 3290462-G-A **
3244215-G-T 3376174-G-T **
3244235-G-T 3376194-G-T **
3275443-G-T 3407402-G-T **
3344613-T-G 3476572-T-G **
3395226-G-T 3527185-G-T **
3456538-C-A 3588497-C-A **
3501083-C-G 3633042-C-G **
3515163-G-T 3647122-G-T FT241099 **
3515316-G-T 3647275-G-T **
3518678-G-T 3650637-G-T **
3568484-C-A 3700443-C-A **
3590406-C-A 3722365-C-A **
3785125-G-T 3917084-G-T **
3841502-G-T 3973461-G-T **
3849133-C-A 3981092-C-A **
3889928-C-A 4021887-C-A **
3967542-A-G 4099501-A-G **
4070060-ATCCT-A 4202019-ATCCT-A **
4125671-G-T 4257630-G-T **
4251281-C-A 4383240-C-A **
4325666-T-C 4457625-T-C **
4326390-A-C 4458349-A-C FT106831 **
4509439-G-C 4641398-G-C **
4900216-T-G 5032175-T-G **
4903062-G-T 5035021-G-T **
5121815-T-G 5253774-T-G **
5163715-C-T 5295674-C-T **
5275452-G-T 5407411-G-T **
5399187-C-A 5531146-C-A **
5591775-G-T 5723734-G-T **
5596594-C-A 5728553-C-A **
5930740-C-A 6062699-C-A **
6191079-A-C 6323038-A-C IR3_Dst **
6368112-C-A 6500071-C-A **
6455065-GA-G 6587024-GA-G 8×A**
6666351-C-A 6798310-C-A **
6682191-T-G 6814150-T-G **
6926395-G-T 7058354-G-T FT107300 **
7015291-A-G 7147250-A-G **
7033541-C-A 7165500-C-A **
7043092-G-T 7175051-G-T **
7081606-G-A 7213565-G-A Y38819 **
7100118-T-G 7232077-T-G **
7135407-TTG-T 7267366-TTG-T **
7158050-A-C 7290009-A-C **
7166430-A-G 7298389-A-G **
7166659-C-A 7298618-C-A **
7183734-CT-C 7315693-CT-C **
7239614-A-C 7371573-A-C **
7254588-C-A 7386547-C-A **
7970383-C-A 8102342-C-A **
8008080-C-A 8140039-C-A **
8100559-A-C 8232518-A-C **
8344279-G-T 8476238-G-T **
8739778-C-A 8871737-C-A **
9094396-T-G 9256787-T-G **
9513235-G-T 9675626-G-T **
9810958-G-T 9973349-G-T **
9913406-C-A 10075797-C-A **
10010586-T-G 10172977-T-G **
10660626-C-A **
10660738-A-T **
10677011-CATTTG-C **
10683060-CTCAAT-C **
10683075-C-T FT185461FT287192 **
10683073-CACTCT-C **
10686683-T-G **
10690234-C-A **
10747986-C-T **
10747990-C-T **
10751723-C-G **
10759809-C-G **
10759812-T-TACTCC **
10784357-TCTCCA-T **
10786804-C-A **
10787313-T-C **
10787333-T-C **
10798325-C-CGATAA **
10798370-C-G **
10802270-G-T **
10812791-C-A **
10819544-T-C **
10822731-A-C **
10822732-A-T **
10861576-T-A **
10878259-C-A **
10878261-T-A **
10878308-C-A **
10878331-C-G **
10885504-T-C **
10885548-C-A **
10888273-A-T **
10901802-C-A **
10929073-C-A **
10930005-A-ATCCCT **
10930041-G-A **
10945423-C-T **
10945445-C-A **
10945454-T-C **
10947506-C-A **
10948329-A-C **
10948352-A-AC **
10948354-TCTATTC-T **
10948378-T-C **
10948393-C-G **
10956111-T-A **
10964932-C-A **
10981466-T-G **
10984849-G-A FT200132 **
10986424-C-A **
10988173-G-A **
11003276-C-T **
11003285-T-A **
11007204-A-G **
11014100-C-A **
11022382-C-A **
11027388-CT-C **
11028270-C-A **
11028279-C-G **
11030599-TGCCAC-T **
11030608-A-G **
11030622-A-T **
11030629-C-T **
11030631-G-C **
13216655-A-C 11060979-A-C **
13227837-G-A 11072161-G-A **
13360939-C-T 11205263-C-T **
13453643-C-T 11297967-C-T **
13453682-C-T 11298006-C-T **
13577947-A-C 11422271-A-C **
13579531-CA-C 11423855-CA-C 23×A**
13579561-C-A 11423885-C-A **
13594438-C-A 11438762-C-A **
13698859-T-A 11543183-T-A **
11648538-C-G **
11648548-A-G **
11649618-AAATGGAATGGAATGGAATGGAATGGAATGG-A **
11651062-G-T **
11655179-C-T **
13884825-A-T 11764119-A-T **
13885516-A-C 11764810-A-C **
13885518-T-C 11764812-T-C **
13901421-C-T 11780715-C-T **
13901532-G-T 11780826-G-T **
13929184-C-A 11808478-C-A **
13995767-C-A 11875061-C-A **
14025676-A-T 11904970-A-T **
14073386-C-A 11952680-C-A **
14142249-C-A 12021543-C-A **
14474540-C-A 12353809-C-A **
14516885-C-A 12405086-C-A **
14531092-T-C 12419293-T-C **
14563060-C-A 12451260-C-A **
14568194-C-A 12456394-C-A **
14686811-G-T 12574877-G-T **
14802944-G-A 12691015-G-A **
15150849-C-A 13038936-C-A **
15157484-A-C 13045571-A-C **
15259219-G-T 13147303-G-T **
15297253-G-T 13185352-G-T **
15297284-A-AT 13185383-A-AT 27×T**
15364681-A-C 13252801-A-C **
15378407-T-G 13266527-T-G **
15536401-ATCC-A 13424521-ATCC-A **
15635983-T-G 13524103-T-G **
15758551-C-A 13646671-C-A **
15792907-C-T 13681027-C-T **
15918464-C-A 13806584-C-A **
16000979-C-A 13889099-C-A FT264211 **
16146485-A-AAGAC 14034605-A-AAGAC P8_Dst **
16226416-A-C 14114536-A-C **
16515969-A-C 14404089-A-C **
16598630-C-A 14486750-C-A **
16682695-A-G 14570815-A-G **
16705588-T-G 14593708-T-G **
16710137-G-T 14598257-G-T **
16896256-T-G 14784376-T-G **
17095797-G-T 14983917-G-T **
17097481-C-A 14985601-C-A **
17218798-C-A 15106918-C-A **
17668261-C-A 15556381-C-A **
17707291-G-A 15595411-G-A **
17864097-G-C 15752217-G-C Y128234 **
18121708-G-T 16009828-G-T **
18152418-G-T 16040538-G-T **
18579650-G-T 16467770-G-T **
18756327-G-T 16644447-G-T **
18790996-G-T 16679116-G-T **
19052089-C-A 16940209-C-A **
19297952-C-A 17186072-C-A **
19529346-C-A 17417466-C-A **
19911451-CAAATTAT-C 17799571-CAAATTAT-C P5_Prx **
20066391-T-C 17954511-T-C Y129973 P5_Gap **
20223236-T-A 18061350-T-A P5_Dst **
20223241-AT-A 18061355-AT-A P5_Dst **
20392168-C-A 18230282-C-A P5_Dst **
20392208-C-A 18230322-C-A P5_Dst **
20569431-T-G 18407545-T-G P5_Dst **
20637720-G-T 18475834-G-T P4_Prx **
21015062-A-G 18853176-A-G P4_Dst **
21015064-A-G 18853178-A-G P4_Dst **
21015066-A-G 18853180-A-G P4_Dst **
21043029-C-A 18881143-C-A **
21201154-C-A 19039268-C-A **
21208830-C-A 19046944-C-A **
21409755-C-T 19247869-C-T **
21990859-G-A 19828973-G-A **
22170229-G-T 20008343-G-T **
22210601-C-A 20048715-C-A **
22788554-C-A 20626668-C-A **
23004195-C-A 20842309-C-A **
23062444-C-A 20900558-C-A **
23362489-A-G 21200603-A-G **
23419264-T-A 21257378-T-A **
23788396-A-C 21626510-A-C **
23875706-C-A 21713820-C-A **
21752316-G-T **
24518568-C-A 22372421-C-A **
24575835-G-T 22429688-G-T P3_t2 **
24869673-A-G 22723526-A-G IR1_R **
25246447-C-CTT 23100300-C-CTT P2_r1 41×T**
25538517-A-C 23392370-A-C P1_gr1 **
25894813-C-A 23748666-C-A P1_Y1 **
27633700-T-G 25487553-T-G P1_Y2 **
28520428-C-A 26374281-C-A **
28608308-C-A 26462161-C-A **
28653869-C-A 26507722-C-A **
28673099-C-A 26526952-C-A **
28763915-C-A 26617768-C-A **
58974376-G-A 56828229-G-A **
56842755-G-T **
56862566-A-C **
19411996-A-AAG 17300116-A-AAG ***
14608231-A-G 12496433-A-G ***
10961593-A-C ***
3116380-C-A 3248339-C-A ***
18138096-C-A 16026216-C-A ***
10767741-C-A ***
9173545-C-A 9335936-C-A ***
11659052-C-A ***
7229020-T-C 7360979-T-C ***
10859114-C-A ***
13453229-CA-C,CG 11297553-CA-C,CG ***
17534376-G-GT,GTT 15422496-G-GT,GTT 12×T***
21043078-A-G 18881192-A-G ***
22594601-G-T 20432715-G-T ***
56827352-C-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.