Harvie

BigY3: 905421
MDKA Birth: Scotland 1706

Tree Position

R-M269 > L23 > L51 > P310 > L151 > S1194 > S1200 > S9977 > 3343814-C-T

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
905421
27502174-C-A 25356027-C-A P1_Y2 A+
13450947-C-T 11295271-C-T A*
58978585-G-A 56832438-G-A A*
3970414-A-G 4102373-A-G A*
4268132-G-T 4400091-G-T A*
4311481-A-C 4443440-A-C A*
13451434-C-A 11295758-C-A A*
58977228-C-A 56831081-C-A A*
59020424-T-C 56874277-T-C A*
19739799-G-GA 17627919-G-GA P5_Prx 16×AA*
58980462-G-T 56834315-G-T A*
58982754-C-T 56836607-C-T A*
13489457-A-G 11333781-A-G A*
56836834-C-T A*
2994613-G-GT 3126572-G-GT 14×TA*
5217168-T-TA 5349127-T-TA 12×AA*
13451197-C-T 11295521-C-T A*
56834539-A-ATTCCG A*
13686980-C-G 11531304-C-G A*
20869021-G-GT 18707135-G-GT P4_Dst 21×TA*
4316442-A-C 4448401-A-C A*
56834432-C-T A*
13450795-C-A 11295119-C-A A*
13450060-T-C 11294384-T-C A*
3727456-A-G 3859415-A-G A*
56832505-T-C A*
10068277-C-A 10230668-C-A FT197469 A*
17987645-C-T 15875765-C-T P7_Prx YA*
22264904-C-A 20103018-C-A DYZ19 A*
27629686-A-C 25483539-A-C P1_Y2 A*
13650712-C-T 11495036-C-T BY210600 5×GGAAT+
22439817-C-T 20277931-C-T FT456336 DYZ19 +
2730241-G-T 2862200-G-T BY192918 YY+
3482982-C-T 3614941-C-T FT194820 +
3731352-T-G 3863311-T-G FT194865 +
3743036-C-A 3874995-C-A FT194867 +
4720688-C-G 4852647-C-G FT195059 +
5653073-C-T 5785032-C-T FT195249 +
6372685-C-T 6504644-C-T BY193050 +
6476572-A-C 6608531-A-C FT195384 +
6834635-C-T 6966594-C-T FT195439 YY+
6860490-A-G 6992449-A-G BY61790 YY+
7072336-G-C 7204295-G-C BY193202 YY+
9425544-A-G 9587935-A-G BY193909 YY+
9847776-A-C 10010167-A-C BY193965 YY+
13925944-A-T 11805238-A-T FT195848 Y+
17418946-A-C 15307066-A-C FT196486 YY+
17578333-C-G 15466453-C-G BY195115 YY+
17756067-A-G 15644187-A-G BY195170 YY+
19078917-C-T 16967037-C-T BY195580 YY+
21039523-GCTGG-C 18877637-GCTGG-C +
21039529-CTTGA-C 18877643-CTTGA-C +
21772247-A-C 19610361-A-C BY195977 YY+
22000622-C-T 19838736-C-T FT197013 Y+
22228624-C-A 20066738-C-A DYZ19 +
22272972-G-A 20111086-G-A BY215499 DYZ19 +
23459843-C-T 21297957-C-T FT197217 YY+
23785729-C-A 21623843-C-A BY196608 Y+
23787439-C-A 21625553-C-A FT197254 +
23989300-G-T 21843153-G-T BY196657 Y+
3940967-A-G 4072926-A-G *
3741749-G-A 3873708-G-A *
28808164-C-T 26662017-C-T BY227434 *
56843981-C-A *
23969674-A-AACAC 21823527-A-AACAC 20×AC*
10976902-G-GCATTC *
3013641-G-T 3145600-G-T *
10068291-T-G 10230682-T-G *
19668850-C-A 17556970-C-A P5_Prx **
20995550-TC-T 18833664-TC-T P4_Dst **
28438230-T-A 26292083-T-A P1_gr2 **
6310843-C-A 6442802-C-A BY196937 IR3_Dst **
27861875-CAAAAAA-C 25715728-CAAAAAA-C P1_Y2 32×A**
6310813-A-T 6442772-A-T IR3_Dst **
16784404-CA-C 14672524-CA-C 18×A**
28081886-AC-A 25935739-AC-A P1_Y2 **
14795080-CTTTT-C 12683151-CTTTT-C 24×T**
11016996-N-A **
20509907-A-C 18348021-A-C P5_Dst **
3394337-CTTT-C 3526296-CTTT-C 21×T**
2946145-G-C 3078104-G-C **
2946148-G-C 3078107-G-C **
5936156-A-C 6068115-A-C **
8481014-C-G 8612973-C-G BY193641 **
9799645-C-G 9962036-C-G **
13250008-G-T 11094332-G-T **
13589105-T-A 11433429-T-A **
15749070-T-C 13637190-T-C **
17638152-A-G 15526272-A-G **
18306820-C-T 16194940-C-T P6_Prx **
19573967-A-AG 17462087-A-AG P5_Prx **
21665713-AAAT-A 19503827-AAAT-A **
22461251-G-T 20299365-G-T BY196159 DYZ19 **
24355728-GAT-G 22209581-GAT-G 9×AT***
13480364-C-T 11324688-C-T ***
2950223-GTA-G 3082182-GTA-G 10×TA***
17787106-CAAA-C 15675226-CAAA-C 19×A***
18125759-G-A 16013879-G-A BY211750 13×GAAA***
4076728-G-GTA 4208687-G-GTA 10×TA***
5178062-CAA-C 5310021-CAA-C 20×A***
28492689-CAA-C 26346542-CAA-C 18×A***
21425339-C-CT 19263453-C-CT 24×T***
13302962-CAA-C 11147286-CAA-C 17×A***
4511163-CAA-C 4643122-CAA-C 26×A***
6808134-C-CA 6940093-C-CA 22×A***
4878246-CAA-C 5010205-CAA-C 18×A***
5453891-CT-C 5585850-CT-C 19×T***
5204877-T-TA 5336836-T-TA 14×A***
5770338-CTT-C 5902297-CTT-C 25×T***
14642454-GTTT-G 12530523-GTTT-G 17×T***
10976934-G-A ***
13709473-A-C 11553797-A-C ***
24389894-C-CT 22243747-C-CT 26×T***
9942043-ATTT-A 10104434-ATTT-A 28×T***
10980697-A-ACCATT ***
14730396-CAAA-C 12618464-CAAA-C 18×A***
2729648-CTTTT-C 2861607-CTTTT-C 25×T***
6989107-TAAA-T,TAA 7121066-TAAA-T,TAA 23×A***
13459310-C-G 11303634-C-G ***
27967336-GTATATA-G 25821189-GTATATA-G P1_Y2 10×TA***
22058321-C-CA 19896435-C-CA 11×A***
13709476-T-A 11553800-T-A ***
19048369-A-G 16936489-A-G ***
4814130-T-TA 4946089-T-TA 9×A***
5270693-CTTTTT-C 5402652-CTTTTT-C 22×T***
5960696-ATT-A 6092655-ATT-A 30×T***
3603491-A-ATT 3735450-A-ATT 24×T***
3299369-CA-C 3431328-CA-C 9×A***
13709483-A-G 11553807-A-G ***
7076281-C-T 7208240-C-T ***
9804497-TG-T 9966888-TG-T ***
13530079-CA-C,CAAA 11374403-CA-C,CAAA 24×A***

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.