Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > DF49/S474 > FGC11210

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
2860915-C-T 2992874-C-T Y38480 YY+
6870063-T-G 7002022-T-G Y38695 YY+
6896791-C-T 7028750-C-T FGC56529 YY+
7094002-G-A 7225961-G-A FGC56530 YY+
9170818-G-A 9333209-G-A FGC56535 Y+
9778041-T-C 9940432-T-C Y40053 Y+
9788762-G-A 9951153-G-A Y40055 Y+
14082301-A-T 11961595-A-T BY54576 YY+
14481002-G-A 12360271-G-A Y40536 YY+
14481004-C-T 12360273-C-T Y40537 YY+
14699465-C-G 12587531-C-G FGC56543 YY+
15447523-G-A 13335643-G-A Y40988 YY+
15589856-C-CAT 13477976-C-CAT +
15753887-G-A 13642007-G-A FGC56545 YY+
15792117-C-A 13680237-C-A FGC56547 YY+
16630246-A-G 14518366-A-G FGC56549 YY+
17603537-C-G 15491657-C-G Y42109 YY+
17606090-T-C 15494210-T-C FGC56551 YY+
17986251-T-C 15874371-T-C Y100895 BY27907 Y+
18200865-C-CA 16088985-C-CA +
18590837-G-T 16478957-G-T FGC56554 YY+
20066584-T-C 17954704-T-C FGC56556 P5_Gap +
21682974-TC-T 19521088-TC-T +
21808761-T-A 19646875-T-A FGC56559 YY+
22103169-G-A 19941283-G-A FGC56560 YY+
22478958-G-C 20317072-G-C BY53225 DYZ19 +
22617588-T-G 20455702-T-G FGC64583 YY+
22907081-C-T 20745195-C-T BY21852 YY+
23079590-C-T 20917704-C-T CTS918FGC56562 YY+
23330057-G-T 21168171-G-T FGC56563 YY+
23371903-A-G 21210017-A-G Y44291 YY+
23615807-T-C 21453921-T-C FGC56565 YY+
13844076-AAAGGT-A 11723370-AAAGGT-A **
26730201-A-AAAAGAAAG 24584054-A-AAAAGAAAG P1_g2 18×AAAG**
17037296-G-T 14925416-G-T Z42904 **
9013031-C-A 9175422-C-A Z272Z296 **
13323760-G-A 11168084-G-A BY85189 **
13936824-A-G 11816118-A-G FGC56537 **
14198118-T-A 12077412-T-A **
15818988-G-T 13707108-G-T **
21880998-G-C 19719112-G-C **
23034379-C-G 20872493-C-G **
13458648-T-C 11302972-T-C ***
13823189-A-G 11702483-A-G ***
27053578-TA-T 24907431-TA-T P1_r4 11×A***
13846547-C-A 11725841-C-A ***
22491129-G-T 20329243-G-T DYZ19 ***
28791582-A-T 26645435-A-T ***
13446512-T-C 11290836-T-C ***
13804931-G-C 11684225-G-C ***
13862157-AATCAG-A 11741451-AATCAG-A ***
13803166-A-G 11682460-A-G ***
13839845-G-T 11719139-G-T ***
13141093-CGTTTT-C,T 10630579-CGTTTT-C,T ***
13862173-A-G 11741467-A-G FT22399 ***
13862185-G-T 11741479-G-T ***
13862204-T-C 11741498-T-C ***
13139296-A-G 10628782-A-G ***
13717331-GAATTA-G 11561655-GAATTA-G ***
9746062-CTCTA-C 9908453-CTCTA-C ***
13454812-C-CAACTG 11299136-C-CAACTG ***
13454827-C-T 11299151-C-T ***
13454833-A-T 11299157-A-T ***
13454846-C-T 11299170-C-T ***
13868229-T-C 11747523-T-C ***
13652195-A-G 11496519-A-G ***
18355098-AT-A 16243218-AT-A P6_Prx 10×T***
13833430-T-G 11712724-T-G ***
13868234-T-C 11747528-T-C ***
10017741-T-C 10180132-T-C ***
13821111-A-G 11700405-A-G ***
25176850-C-CT 23030703-C-CT g1 30×T***
28813293-T-G 26667146-T-G ***
13862205-C-T 11741499-C-T ***
16108648-G-A 13996768-G-A P8_Prx ***
24016986-CT-C 21870839-CT-C 15×T***
28799850-G-T 26653703-G-T ***
13858584-G-C 11737878-G-C ***
20206684-GA-G 18044798-GA-G P5_Dst 9×A***
10017707-C-CT 10180098-C-CT ***
13810176-A-T 11689470-A-T ***
16157706-GAAAGA-G 14045826-GAAAGA-G P8_Dst 6×AAAGA***
13453735-T-C 11298059-T-C ***
13858582-A-C 11737876-A-C ***
16148183-C-CT 14036303-C-CT P8_Dst 27×T***
13832610-C-A 11711904-C-A ***
22353081-T-C 20191195-T-C DYZ19 ***
13331833-G-A 11176157-G-A ***
58974101-G-C 56827954-G-C ***
13805376-G-A 11684670-G-A ***
13450096-C-T 11294420-C-T ***
13450189-T-C 11294513-T-C ***
13458431-CACTCGGAATG-C 11302755-CACTCGGAATG-C ***
13647930-G-T 11492254-G-T ***
13647945-C-T 11492269-C-T BY210570BY210570 ***
13652130-G-A,GTGGAA 11496454-G-A,GTGGAA 11×TGGAA***
13695999-G-A 11540323-G-A ***
13703861-G-C 11548185-G-C ***
13713567-G-A 11557891-G-A BY89538 ***
13801073-T-G 11680367-T-G ***
13801160-A-C 11680454-A-C ***
13801163-G-C 11680457-G-C ***
13838012-G-A 11717306-G-A ***
13859964-A-AGAATG 11739258-A-AGAATG ***
13859975-G-A 11739269-G-A ***
13859982-A-G 11739276-A-G ***
13862165-G-C 11741459-G-C ***
13862166-G-A 11741460-G-A ***
13865775-G-C 11745069-G-C ***
13867973-A-G 11747267-A-G ***
13868401-G-A 11747695-G-A ***
16108664-T-A 13996784-T-A P8_Prx ***
18291849-C-T 16179969-C-T P6_Prx ***
18347957-C-T 16236077-C-T P6_Prx ***
19816601-T-TA 17704721-T-TA P5_Prx 8×A***
19871271-T-G 17759391-T-G P5_Prx ***
20884101-G-GA 18722215-G-GA P4_Dst 10×A***
22147729-T-C 19985843-T-C ***
22242547-C-G 20080661-C-G DYZ19 ***
22250865-T-A 20088979-T-A DYZ19 ***
22274285-C-T 20112399-C-T DYZ19 ***
22278659-C-A 20116773-C-A DYZ19 ***
22291406-C-T 20129520-C-T DYZ19 ***
22317135-G-C 20155249-G-C DYZ19 ***
22343731-G-T 20181845-G-T DYZ19 ***
22422766-G-C 20260880-G-C DYZ19 ***
22448422-T-A 20286536-T-A DYZ19 ***
22452572-G-T 20290686-G-T DYZ19 ***
22455419-G-C 20293533-G-C DYZ19 ***
22456527-G-T 20294641-G-T DYZ19 ***
24108798-C-T 21962651-C-T P3_b1 ***
24143078-A-T 21996931-A-T P3_b1 ***
24820454-G-A 22674307-G-A P3_b2 ***
24941082-C-T 22794935-C-T FGC56567 g1 ***
26440525-T-A 24294378-T-A BY30220 P1_Y1 10×TTTA***
27150720-AT-A,ATT 25004573-AT-A,ATT P1_g3 12×T***
28784443-G-T 26638296-G-T ***
58866148-G-C 56724723-C-G ***
13833375-TG-A,AG 11712669-TG-A,AG ***
13862171-T-A,G 11741465-T-A,G ***
13469897-G-A,C 11314221-G-A,C ***
13470649-T-C,G 11314973-T-C,G ***
13810817-G-C,T 11690111-G-C,T ***

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.