Haldane

FTDNA: 263323, BigY3: 263323
MDKA Birth: Scotland

Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF63/S522 > BY711

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
263323		BigY3
263323		Manual
Edits
22436329-T-C 20274443-T-C DYZ19 ***A*
6326859-C-T 6458818-C-T IR3_Dst ***A*
18380279-G-A 16268399-G-A P6_Prx ***A*
19606376-C-T 17494496-C-T P5_Prx Y***A*
19636377-C-T 17524497-C-T P5_Prx ***A*
20027159-G-C 17915279-G-C P5_Prx ***A*
20624744-G-A 18462858-G-A P4_Prx ***A*
24305644-G-A 22159497-G-A P3_t1 ***A*
26146043-A-G 23999896-A-G P1_Y1 ***A*
26380199-A-T 24234052-A-T P1_Y1 ***A*
19921051-C-T 17809171-C-T P5_Prx A*
24263074-C-A 22116927-C-A P3_b1 A*
15759868-G-T 13647988-G-T CTS4665 Y+
6121105-G-C 6253064-G-C FGC81832 +
7066801-T-C 7198760-T-C FGC51560 YY++
7354694-C-T 7486653-C-T FGC51562 YY++
8891837-TC-T 9023796-TC-T ++
9162403-T-G 9324794-T-G FGC51563 ++
13715828-C-T 11560152-C-T FGC81833 +
14171510-C-T 12050804-C-T FGC51564 YY+**
14194090-G-A 12073384-G-A FGC51565 YY++
14215523-A-G 12094817-A-G FGC51566 YY++
14498140-G-T 12386345-G-T FGC51567 YY++
14804545-A-G 12692616-A-G FGC51568 YY++
15840817-G-A 13728937-G-A FGC51569 YY++
16669858-A-G 14557978-A-G FGC81834 YY++
16893061-GA-G 14781181-GA-G ++
17121212-G-A 15009332-G-A FGC51570 YY++
18028595-C-T 15916715-C-T FGC51571 Y++
18234959-G-A 16123079-G-A FGC51572 Y++
18880713-G-A 16768833-G-A FGC51573 YY++
19047713-C-A 16935833-C-A FGC51574 YY++
20820146-G-A 18658260-G-A FGC51575 P4_Gap ++
21724641-G-T 19562755-G-T FGC51576 YY++
21871399-C-T 19709513-C-T FGC51577 YY++
21892106-T-A 19730220-T-A FGC81835 YY++
22246290-T-C 20084404-T-C FGC51578 DYZ19 +
22471328-T-A 20309442-T-A FGC51579 DYZ19 +**
22771028-T-C 20609142-T-C FGC51581 YY++
22958736-A-C 20796850-A-C FGC51582 YY++
23131580-G-A 20969694-G-A FGC51583 YY++
23310143-G-T 21148257-G-T FGC51584 YY++
23554883-T-G 21392997-T-G FGC63879 YY++
23604472-C-T 21442586-C-T FGC51585 YY++
3675031-G-C 3806990-G-C FT88354 +
3821669-A-G 3953628-A-G FGC81830 +
4876731-A-G 5008690-A-G FT88671 +
5902436-G-C 6034395-G-C FT88905 +
7340332-G-A 7472291-G-A YY+
10789604-C-A FT183070 +
10975910-C-T FT183069 +
13642370-C-T 11486694-C-T FT179 +
11664151-G-T FT450826 +
18614020-G-A 16502140-G-A FT89548 YY+
24523489-GA-G 22377342-GA-G +
28666619-G-A 26520472-G-A FT11405 +
22302205-G-T 20140319-G-T DYZ19 ****
18556556-CTGTG-C,CTG 16444676-CTGTG-C,CTG 15×TG*
22351276-A-G 20189390-A-G DYZ19 **
22351368-T-A 20189482-T-A DYZ19 **
22351379-G-A 20189493-G-A DYZ19 **
17644195-A-T 15532315-A-T **
22351283-T-A 20189397-T-A DYZ19 **
22351360-C-G 20189474-C-G DYZ19 **
22446493-A-G 20284607-A-G BY52707 DYZ19 *****
13523495-C-A 11367819-C-A **
28545901-G-A 26399754-G-A **
13808703-T-A 11687997-T-A **
10991-T-C FGC81829 **
15636237-C-T 13524357-C-T FTB21367 **
2677528-A-G 2809487-A-G **
2697927-A-G 2829886-A-G **
4212180-G-A 4344139-G-A FT148410 **
4725564-G-T 4857523-G-T **
5015122-G-A 5147081-G-A FT148521 **
8826530-C-CGGG 8958489-C-CGGG **
9373563-T-C 9535954-T-C **
9513423-G-C 9675814-G-C **
13523493-G-T 11367817-G-T **
13627450-C-T 11471774-C-T **
19019632-T-C 16907752-T-C **
19537902-A-T 17426022-A-T **
21589311-A-G 19427425-A-G **
22446564-T-C 20284678-T-C DYZ19 **
22692786-G-A 20530900-G-A **
21753939-A-G **
9955109-C-T 10117500-C-T ***
22224654-T-A 20062768-T-A DYZ19 ***
22262007-C-G 20100121-C-G DYZ19 ***
22269391-G-T 20107505-G-T DYZ19 ******
22281796-G-T 20119910-G-T DYZ19 ***
22290151-G-C 20128265-G-C DYZ19 ***
22290154-A-C 20128268-A-C DYZ19 ***
22290163-G-C 20128277-G-C DYZ19 ***
22291235-A-G 20129349-A-G BY10479 DYZ19 ***
22291259-A-G 20129373-A-G DYZ19 ***
22300516-T-C 20138630-T-C DYZ19 ***
22426352-T-A 20264466-T-A DYZ19 ***
22441448-A-G 20279562-A-G DYZ19 ******
22442056-T-A 20280170-T-A DYZ19 ***
24974044-C-T 22827897-C-T g1 ***
25041912-C-T 22895765-C-T g1 ***
25100385-T-C 22954238-T-C g1 ***
25183709-G-T 23037562-G-T g1 ***
26202564-C-T 24056417-C-T P1_Y1 ***
8504198-T-TTGTG 8636157-T-TTGTG 19×TG***
22479696-T-G 20317810-T-G DYZ19 ***
17165269-A-G 15053389-A-G ***
15969956-TA-T,TAA 13858076-TA-T,TAA 20×A***
19073887-C-T 16962007-C-T ***
17946803-AT-A 15834923-AT-A 9×T***
22893570-C-T 20731684-C-T ***
15733708-C-CAA 13621828-C-CAA 11×A***
13460204-C-A 11304528-C-A ***
15865946-CTTTTTTTTTTTTT-C 13754066-CTTTTTTTTTTTTT-C 37×T***
16265038-GA-G 14153158-GA-G 9×A***
5650593-A-AACACAC 5782552-A-AACACAC 18×AC***
2740644-C-G 2872603-C-G ***
3474543-C-CA,CAAA 3606502-C-CA,CAAA 15×A***
4392213-A-G 4524172-A-G ***
5368550-A-G 5500509-A-G ***
5448435-T-A 5580394-T-A ***
6664880-GT-G 6796839-GT-G 10×T***
7309743-C-A 7441702-C-A ***
8428944-CAAAA-C,CAA 8560903-CAAAA-C,CAA 25×A***
9402766-T-C 9565157-T-C ***
11023147-C-T ***
13476128-A-G 11320452-A-G ***
14450557-A-G 12329830-A-G ***
14458416-C-T 12337689-C-T ***
14682366-G-A 12570432-G-A ***
14882153-C-T 12770221-C-T ***
15045159-GTT-G 12933249-GTT-G ***
15477176-T-C 13365296-T-C ***
15685824-A-T 13573944-A-T ***
15750589-C-A 13638709-C-A ***
16364133-C-T 14252253-C-T ***
16896308-A-G 14784428-A-G ***
21235244-AAAG-T 19073358-AAAG-T ***
21989007-T-C 19827121-T-C ***
22479677-A-T 20317791-A-T DYZ19 ***
22479689-G-T 20317803-G-T DYZ19 ***
22479693-A-T 20317807-A-T DYZ19 ***
22479708-G-T 20317822-G-T DYZ19 ***
22974138-AAAT-A,AAT 20812252-AAAT-A,AAT ***
23036190-T-C 20874304-T-C ***
23350626-CTTTTTTT-C,CTTTTTT 21188740-CTTTTTTT-C,CTTTTTT 21×T***
23431507-A-G 21269621-A-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
Manual28633264-G-T26487117-G-T14T
Manual7502928-C-CT7634887-C-CTAbout 200 reads without the insertion and about 64 with.
Manual8029414-A-AT8161373-A-AT33 reads show the insertion, 2 of which actually show a 2T insertion.